rs10205049

Variant names:

• chr2-119142357-G-A
• rs10205049

Variant summary

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

The variant allele was found at a frequency of 0.483 in 151,904 control chromosomes in the GnomAD database, including 18,584 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 0.48 (18584 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.128
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.565 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: 0.483 AC: 73264 AN: 151786 Hom.: 18579 Cov.: 32

Gnomad AFR AF: 0.365

Gnomad AMI AF: 0.360

Gnomad AMR AF: 0.521

Gnomad ASJ AF: 0.528

Gnomad EAS AF: 0.139

Gnomad SAS AF: 0.465

Gnomad FIN AF: 0.501

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.570

Gnomad OTH AF: 0.475

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

GnomAD4 genome AF: 0.483 AC: 73296 AN: 151904 Hom.: 18584 Cov.: 32 AF XY: 0.478 AC XY: 35498 AN XY: 74222

African (AFR) AF: 0.364 AC: 15074 AN: 41368

American (AMR) AF: 0.522 AC: 7973 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.528 AC: 1831 AN: 3470

East Asian (EAS) AF: 0.138 AC: 711 AN: 5162

South Asian (SAS) AF: 0.466 AC: 2241 AN: 4806

European-Finnish (FIN) AF: 0.501 AC: 5288 AN: 10546

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.570 AC: 38717 AN: 67960

Other (OTH) AF: 0.473 AC: 998 AN: 2108

Alfa AF: 0.532 Hom.: 33830

Bravo AF: 0.474

Asia WGS AF: 0.304 AC: 1060 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.6
DANN	Benign	0.55
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs10205049; hg19: chr2-119899933; COSMIC: COSV60101441;