rs990171

Positions:

• chr2-102470310-A-C
• chr2-102470310-A-G

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 0.777 in 152,106 control chromosomes in the GnomAD database, including 46,902 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 0.78 (46902 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.400

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.894 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.777 AC: 118033 AN: 151988 Hom.: 46859 Cov.: 32

Gnomad AFR AF: 0.902

Gnomad AMI AF: 0.741

Gnomad AMR AF: 0.606

Gnomad ASJ AF: 0.767

Gnomad EAS AF: 0.551

Gnomad SAS AF: 0.560

Gnomad FIN AF: 0.812

Gnomad MID AF: 0.759

Gnomad NFE AF: 0.767

Gnomad OTH AF: 0.755

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

GnomAD4 genome AF: 0.777 AC: 118125 AN: 152106 Hom.: 46902 Cov.: 32 AF XY: 0.771 AC XY: 57305 AN XY: 74340

Gnomad4 AFR AF: 0.902

Gnomad4 AMR AF: 0.605

Gnomad4 ASJ AF: 0.767

Gnomad4 EAS AF: 0.552

Gnomad4 SAS AF: 0.560

Gnomad4 FIN AF: 0.812

Gnomad4 NFE AF: 0.767

Gnomad4 OTH AF: 0.757

Alfa AF: 0.738 Hom.: 8208

Bravo AF: 0.766

Asia WGS AF: 0.579 AC: 2016 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.96
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs990171; hg19: chr2-103086770; COSMIC: COSV54830565;