chr2-136548407-T-C

Variant names:

• chr2-136548407-T-C
• rs10496749
• ENST00000803876.1:n.161-1702A>G

Variant summary

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

The ENST00000803876.1(ENSG00000304503):​n.161-1702A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.172 in 152,074 control chromosomes in the GnomAD database, including 2,649 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 0.17 (2649 hom., cov: 32)
• Consequence: ENSG00000304503 ENST00000803876.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.54
• Publications: 3 publications found

Genes affected

ENSG00000304503 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.401 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000803876.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000304503	ENST00000803876.1		n.161-1702A>G		intron	N/A
	ENSG00000304503	ENST00000803877.1		n.158-3503A>G		intron	N/A
	ENSG00000304503	ENST00000803878.1		n.242-1702A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.172 AC: 26169 AN: 151956 Hom.: 2645 Cov.: 32

Gnomad AFR AF: 0.149

Gnomad AMI AF: 0.102

Gnomad AMR AF: 0.293

Gnomad ASJ AF: 0.155

Gnomad EAS AF: 0.415

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.183

Gnomad MID AF: 0.239

Gnomad NFE AF: 0.136

Gnomad OTH AF: 0.187

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

GnomAD4 genome AF: 0.172 AC: 26191 AN: 152074 Hom.: 2649 Cov.: 32 AF XY: 0.179 AC XY: 13326 AN XY: 74328

African (AFR) AF: 0.149 AC: 6197 AN: 41482

American (AMR) AF: 0.294 AC: 4492 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.155 AC: 539 AN: 3470

East Asian (EAS) AF: 0.416 AC: 2143 AN: 5156

South Asian (SAS) AF: 0.223 AC: 1075 AN: 4820

European-Finnish (FIN) AF: 0.183 AC: 1937 AN: 10576

Middle Eastern (MID) AF: 0.233 AC: 68 AN: 292

European-Non Finnish (NFE) AF: 0.136 AC: 9256 AN: 67984

Other (OTH) AF: 0.186 AC: 392 AN: 2110

Alfa AF: 0.0816 Hom.: 126

Bravo AF: 0.183

Asia WGS AF: 0.319 AC: 1108 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.8
DANN	Benign	0.53
PhyloP100		1.5

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: rs10496749;

hg19: chr2-137305977;