2-149036100-T-C

Variant names:

• chr2-149036100-T-C
• rs10929935
• ENST00000743804.1:n.162A>G

Variant summary

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

The ENST00000743804.1(ENSG00000296946):​n.162A>G 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 0.313 in 151,894 control chromosomes in the GnomAD database, including 8,350 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 0.31 (8350 hom., cov: 31)
• Consequence: ENSG00000296946 ENST00000743804.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0680
• Publications: 2 publications found

Genes affected

ENSG00000296946 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.664 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000296946	ENST00000743804.1	n.162A>G		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.314 AC: 47611 AN: 151778 Hom.: 8350 Cov.: 31

Gnomad AFR AF: 0.180

Gnomad AMI AF: 0.431

Gnomad AMR AF: 0.325

Gnomad ASJ AF: 0.300

Gnomad EAS AF: 0.684

Gnomad SAS AF: 0.308

Gnomad FIN AF: 0.345

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.359

Gnomad OTH AF: 0.311

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

GnomAD4 genome AF: 0.313 AC: 47612 AN: 151894 Hom.: 8350 Cov.: 31 AF XY: 0.315 AC XY: 23341 AN XY: 74198

African (AFR) AF: 0.180 AC: 7447 AN: 41440

American (AMR) AF: 0.325 AC: 4955 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.300 AC: 1040 AN: 3470

East Asian (EAS) AF: 0.683 AC: 3522 AN: 5156

South Asian (SAS) AF: 0.307 AC: 1480 AN: 4818

European-Finnish (FIN) AF: 0.345 AC: 3631 AN: 10516

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.359 AC: 24400 AN: 67934

Other (OTH) AF: 0.315 AC: 665 AN: 2112

Alfa AF: 0.342 Hom.: 17242

Bravo AF: 0.311

Asia WGS AF: 0.441 AC: 1534 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.0
DANN	Benign	0.47
PhyloP100		0.068

Splicing

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

Other links and lift over

dbSNP: rs10929935; hg19: chr2-149892614;