rs2279263

Variant names:

• chr17-20895806-A-G
• rs2279263
• ENST00000327925.7:n.358T>C

Your query was ambiguous. Multiple possible variants found:

• chr17-20895806-A-G
• chr17-20895806-A-T

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The ENST00000327925.7(CCDC144NL):​n.358T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.494 in 1,593,096 control chromosomes in the GnomAD database, including 199,409 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.54 (22523 hom., cov: 32)
  • Exomes 𝑓: 0.49 (176886 hom.)
• Consequence: CCDC144NL ENST00000327925.7 non_coding_transcript_exon
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.376
• Publications: 14 publications found

Genes affected

CCDC144NL (HGNC:):

CCDC144NL-AS1 (HGNC:51340): (CCDC144NL antisense RNA 1)

CCDC144NL (HGNC:33735): (CCDC144A N-terminal like (pseudogene))

ACMG classification

Our verdict: Benign. The variant received -20 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=2.401482E-6).
• BP6: Variant 17-20895806-A-G is Benign according to our data. Variant chr17-20895806-A-G is described in ClinVar as Benign. ClinVar VariationId is 769432.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.665 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000327925.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC144NL	NR_164128.1		n.358T>C		non_coding_transcript_exon	Exon 1 of 4
	CCDC144NL-AS1	NR_104185.2		n.362+3374A>G		intron	N/A
	CCDC144NL-AS1	NR_160710.1		n.620+3374A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC144NL	ENST00000327925.7	TSL:1	n.358T>C		non_coding_transcript_exon	Exon 1 of 4
	CCDC144NL-AS1	ENST00000583962.3	TSL:1	n.424+3374A>G		intron	N/A
	CCDC144NL	ENST00000647562.3		n.215T>C		non_coding_transcript_exon	Exon 1 of 2

Frequencies

GnomAD3 genomes AF: 0.539 AC: 81756 AN: 151764 Hom.: 22502 Cov.: 32

Gnomad AFR AF: 0.671

Gnomad AMI AF: 0.446

Gnomad AMR AF: 0.488

Gnomad ASJ AF: 0.472

Gnomad EAS AF: 0.496

Gnomad SAS AF: 0.444

Gnomad FIN AF: 0.510

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.489

Gnomad OTH AF: 0.525

GnomAD2 exomes AF: 0.489 AC: 118148 AN: 241420 AF XY: 0.484

Gnomad AFR exome AF: 0.670

Gnomad AMR exome AF: 0.472

Gnomad ASJ exome AF: 0.461

Gnomad EAS exome AF: 0.487

Gnomad FIN exome AF: 0.516

Gnomad NFE exome AF: 0.482

Gnomad OTH exome AF: 0.475

GnomAD4 exome AF: 0.490 AC: 705909 AN: 1441214 Hom.: 176886 Cov.: 63 AF XY: 0.488 AC XY: 349265 AN XY: 716230

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.678 AC: 22374 AN: 32978

American (AMR) AF: 0.477 AC: 21095 AN: 44262

Ashkenazi Jewish (ASJ) AF: 0.463 AC: 11977 AN: 25894

East Asian (EAS) AF: 0.525 AC: 20832 AN: 39648

South Asian (SAS) AF: 0.439 AC: 37593 AN: 85596

European-Finnish (FIN) AF: 0.510 AC: 27176 AN: 53252

Middle Eastern (MID) AF: 0.506 AC: 2687 AN: 5308

European-Non Finnish (NFE) AF: 0.487 AC: 532892 AN: 1094696

Other (OTH) AF: 0.491 AC: 29283 AN: 59580

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome AF: 0.539 AC: 81821 AN: 151882 Hom.: 22523 Cov.: 32 AF XY: 0.536 AC XY: 39802 AN XY: 74236

African (AFR) AF: 0.672 AC: 27785 AN: 41366

American (AMR) AF: 0.488 AC: 7451 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.472 AC: 1637 AN: 3470

East Asian (EAS) AF: 0.495 AC: 2551 AN: 5150

South Asian (SAS) AF: 0.443 AC: 2126 AN: 4804

European-Finnish (FIN) AF: 0.510 AC: 5383 AN: 10562

Middle Eastern (MID) AF: 0.514 AC: 151 AN: 294

European-Non Finnish (NFE) AF: 0.489 AC: 33222 AN: 67942

Other (OTH) AF: 0.526 AC: 1109 AN: 2110

Alfa AF: 0.500 Hom.: 9675

Bravo AF: 0.542

ExAC AF: 0.489 AC: 59330

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	2	not provided (2)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.024
BayesDel_addAF	Benign	-0.77	T
BayesDel_noAF	Benign	-0.74
CADD	Benign	3.1
DANN	Benign	0.45
DEOGEN2	Benign	0.00095	T
Eigen	Benign	-2.0
Eigen_PC	Benign	-2.1
FATHMM_MKL	Benign	0.00080	N
LIST_S2	Benign	0.27	T
MetaRNN	Benign	0.0000024	T
MetaSVM	Benign	-0.96	T
MutationAssessor	Benign	-1.9	N
PhyloP100		-0.38
PrimateAI	Uncertain	0.51	T
Polyphen		0.0	B
ClinPred		0.0017	T
GERP RS		-1.3
Varity_R		0.072
gMVP		0.028
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.050		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2279263; hg19: chr17-20799119; COSMIC: COSV60000293; COSMIC: COSV60000293;