rs2190093

Variant names:

• chr7-106658958-A-G
• rs2190093
• NM_175884.6:c.*1231T>C

Your query was ambiguous. Multiple possible variants found:

• chr7-106658958-A-G
• chr7-106658958-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_175884.6(CCDC71L):​c.*1231T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.151 in 152,188 control chromosomes in the GnomAD database, including 2,375 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.15 (2375 hom., cov: 32)
  • Exomes 𝑓: 0.11 (0 hom.)
• Consequence: CCDC71L NM_175884.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.180
• Publications: 6 publications found

Genes affected

CCDC71L (HGNC:26685): (coiled-coil domain containing 71 like) Predicted to be involved in cellular lipid metabolic process and positive regulation of fat cell differentiation. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000243797 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.514 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC71L	NM_175884.6	c.*1231T>C		3_prime_UTR_variant	Exon 1 of 1	ENST00000523505.3	NP_787080.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC71L	ENST00000523505.3	c.*1231T>C		3_prime_UTR_variant	Exon 1 of 1	6	NM_175884.6	ENSP00000430897.2
ENSG00000243797	ENST00000490856.5	n.109-48495T>C		intron_variant	Intron 1 of 4	4
ENSG00000243797	ENST00000592441.1	n.173-48495T>C		intron_variant	Intron 2 of 4	2

Frequencies

GnomAD3 genomes AF: 0.151 AC: 22924 AN: 152040 Hom.: 2379 Cov.: 32

Gnomad AFR AF: 0.0566

Gnomad AMI AF: 0.181

Gnomad AMR AF: 0.158

Gnomad ASJ AF: 0.158

Gnomad EAS AF: 0.530

Gnomad SAS AF: 0.323

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.162

Gnomad OTH AF: 0.128

GnomAD4 exome AF: 0.107 AC: 3 AN: 28 Hom.: 0 Cov.: 0 AF XY: 0.125 AC XY: 1 AN XY: 8

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.115 AC: 3 AN: 26

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AF: 0.00 AC: 0 AN: 2

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.022510), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome AF: 0.151 AC: 22921 AN: 152160 Hom.: 2375 Cov.: 32 AF XY: 0.154 AC XY: 11451 AN XY: 74358

African (AFR) AF: 0.0565 AC: 2346 AN: 41538

American (AMR) AF: 0.157 AC: 2407 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.158 AC: 548 AN: 3468

East Asian (EAS) AF: 0.530 AC: 2734 AN: 5156

South Asian (SAS) AF: 0.324 AC: 1562 AN: 4820

European-Finnish (FIN) AF: 0.177 AC: 1874 AN: 10584

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.162 AC: 10993 AN: 67978

Other (OTH) AF: 0.127 AC: 269 AN: 2114

Alfa AF: 0.151 Hom.: 2567

Bravo AF: 0.145

Asia WGS AF: 0.406 AC: 1410 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	4.5
DANN	Benign	0.71
PhyloP100		0.18
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs2190093; hg19: chr7-106299404;