rs10179195

Variant names:

• chr2-85535638-A-G
• rs10179195

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 0.505 in 151,992 control chromosomes in the GnomAD database, including 20,055 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 0.50 (20055 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.913

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.64 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: 0.505 AC: 76637 AN: 151874 Hom.: 20036 Cov.: 32

Gnomad AFR AF: 0.647

Gnomad AMI AF: 0.459

Gnomad AMR AF: 0.425

Gnomad ASJ AF: 0.396

Gnomad EAS AF: 0.390

Gnomad SAS AF: 0.395

Gnomad FIN AF: 0.456

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.467

Gnomad OTH AF: 0.504

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

GnomAD4 genome AF: 0.505 AC: 76703 AN: 151992 Hom.: 20055 Cov.: 32 AF XY: 0.502 AC XY: 37263 AN XY: 74278

Gnomad4 AFR AF: 0.647

Gnomad4 AMR AF: 0.424

Gnomad4 ASJ AF: 0.396

Gnomad4 EAS AF: 0.390

Gnomad4 SAS AF: 0.396

Gnomad4 FIN AF: 0.456

Gnomad4 NFE AF: 0.467

Gnomad4 OTH AF: 0.506

Alfa AF: 0.468 Hom.: 6996

Bravo AF: 0.507

Asia WGS AF: 0.434 AC: 1509 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.8
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10179195; hg19: chr2-85762761;