1-165708436-C-T

Variant names:

• chr1-165708436-C-T
• rs12027066
• ENST00000400982.2:n.408-139C>T

Variant summary

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

The ENST00000453762.1(ENSG00000215838):​n.154C>T 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 0.082 in 215,150 control chromosomes in the GnomAD database, including 1,964 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 0.079 (1338 hom., cov: 31)
  • Exomes 𝑓: 0.090 (626 hom.)
• Consequence: ENSG00000215838 ENST00000453762.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.03
• Publications: 2 publications found

Genes affected

ENSG00000293132 (HGNC:58646):

ENSG00000215838 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.595 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000453762.1. 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
	CA14P1	NR_036683.1		n.408-139C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000293132	ENST00000400982.2	TSL:1	n.408-139C>T		intron	N/A
	ENSG00000215838	ENST00000453762.1	TSL:6	n.154C>T		non_coding_transcript_exon	Exon 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0786 AC: 11956 AN: 152064 Hom.: 1336 Cov.: 31

Gnomad AFR AF: 0.0407

Gnomad AMI AF: 0.0373

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.0490

Gnomad EAS AF: 0.612

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.0939

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0522

Gnomad OTH AF: 0.0779

GnomAD4 exome AF: 0.0904 AC: 5691 AN: 62968 Hom.: 626 Cov.: 0 AF XY: 0.0889 AC XY: 3156 AN XY: 35508

African (AFR) AF: 0.0392 AC: 55 AN: 1404

American (AMR) AF: 0.174 AC: 715 AN: 4098

Ashkenazi Jewish (ASJ) AF: 0.0462 AC: 48 AN: 1040

East Asian (EAS) AF: 0.605 AC: 1485 AN: 2454

South Asian (SAS) AF: 0.104 AC: 833 AN: 7978

European-Finnish (FIN) AF: 0.0810 AC: 523 AN: 6460

Middle Eastern (MID) AF: 0.0758 AC: 135 AN: 1782

European-Non Finnish (NFE) AF: 0.0480 AC: 1659 AN: 34578

Other (OTH) AF: 0.0750 AC: 238 AN: 3174

GnomAD4 genome AF: 0.0786 AC: 11958 AN: 152182 Hom.: 1338 Cov.: 31 AF XY: 0.0832 AC XY: 6188 AN XY: 74382

African (AFR) AF: 0.0407 AC: 1692 AN: 41528

American (AMR) AF: 0.106 AC: 1613 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0490 AC: 170 AN: 3472

East Asian (EAS) AF: 0.612 AC: 3149 AN: 5142

South Asian (SAS) AF: 0.118 AC: 571 AN: 4824

European-Finnish (FIN) AF: 0.0939 AC: 995 AN: 10592

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0522 AC: 3549 AN: 68024

Other (OTH) AF: 0.0771 AC: 163 AN: 2114

Alfa AF: 0.0609 Hom.: 742

Bravo AF: 0.0829

Asia WGS AF: 0.296 AC: 1030 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	14
DANN	Benign	0.76
PhyloP100		1.0

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs12027066;

hg19: chr1-165677673;

COSMIC: COSV68953257;