2-136149600-A-C

Variant names:

• chr2-136149600-A-C
• rs953387
• ENST00000805101.1:n.685+22150A>C

Variant summary

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

The ENST00000805101.1(ENSG00000304642):​n.685+22150A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.414 in 151,984 control chromosomes in the GnomAD database, including 14,354 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 0.41 (14354 hom., cov: 31)
• Consequence: ENSG00000304642 ENST00000805101.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0590
• Publications: 13 publications found

Genes affected

ENSG00000304642 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.755 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000805101.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000304642	ENST00000805101.1		n.685+22150A>C		intron	N/A
	ENSG00000304642	ENST00000805102.1		n.142-6723A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.414 AC: 62914 AN: 151866 Hom.: 14334 Cov.: 31

Gnomad AFR AF: 0.444

Gnomad AMI AF: 0.333

Gnomad AMR AF: 0.519

Gnomad ASJ AF: 0.727

Gnomad EAS AF: 0.775

Gnomad SAS AF: 0.510

Gnomad FIN AF: 0.335

Gnomad MID AF: 0.775

Gnomad NFE AF: 0.332

Gnomad OTH AF: 0.493

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.414 AC: 62995 AN: 151984 Hom.: 14354 Cov.: 31 AF XY: 0.423 AC XY: 31400 AN XY: 74276

African (AFR) AF: 0.445 AC: 18426 AN: 41450

American (AMR) AF: 0.519 AC: 7924 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.727 AC: 2522 AN: 3470

East Asian (EAS) AF: 0.775 AC: 3993 AN: 5152

South Asian (SAS) AF: 0.509 AC: 2446 AN: 4802

European-Finnish (FIN) AF: 0.335 AC: 3546 AN: 10572

Middle Eastern (MID) AF: 0.765 AC: 225 AN: 294

European-Non Finnish (NFE) AF: 0.332 AC: 22559 AN: 67950

Other (OTH) AF: 0.499 AC: 1051 AN: 2108

Alfa AF: 0.388 Hom.: 25914

Bravo AF: 0.427

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.6
DANN	Benign	0.56
PhyloP100		0.059

Splicing

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

Other links and lift over

dbSNP: rs953387; hg19: chr2-136907170;