chr2-149036100-T-C

Variant names:

• chr2-149036100-T-C
• rs10929935

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0680

ACMG classification

Verdict is Benign. Variant got -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

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

Gnomad4 AFR AF: 0.180

Gnomad4 AMR AF: 0.325

Gnomad4 ASJ AF: 0.300

Gnomad4 EAS AF: 0.683

Gnomad4 SAS AF: 0.307

Gnomad4 FIN AF: 0.345

Gnomad4 NFE AF: 0.359

Gnomad4 OTH AF: 0.315

Alfa AF: 0.337 Hom.: 4253

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10929935; hg19: chr2-149892614;