rs2102860

Variant names:

• chr3-187393195-G-A
• rs2102860

Your query was ambiguous. Multiple possible variants found:

• chr3-187393195-G-A
• chr3-187393195-G-T

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 0.943 in 152,332 control chromosomes in the GnomAD database, including 67,820 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 0.94 (67820 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.539

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.974 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: 0.943 AC: 143536 AN: 152214 Hom.: 67773 Cov.: 34

Gnomad AFR AF: 0.900

Gnomad AMI AF: 0.911

Gnomad AMR AF: 0.967

Gnomad ASJ AF: 0.969

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.980

Gnomad FIN AF: 0.953

Gnomad MID AF: 0.984

Gnomad NFE AF: 0.954

Gnomad OTH AF: 0.949

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

GnomAD4 genome AF: 0.943 AC: 143641 AN: 152332 Hom.: 67820 Cov.: 34 AF XY: 0.943 AC XY: 70266 AN XY: 74482

Gnomad4 AFR AF: 0.900

Gnomad4 AMR AF: 0.967

Gnomad4 ASJ AF: 0.969

Gnomad4 EAS AF: 0.997

Gnomad4 SAS AF: 0.980

Gnomad4 FIN AF: 0.953

Gnomad4 NFE AF: 0.954

Gnomad4 OTH AF: 0.949

Alfa AF: 0.943 Hom.: 9620

Bravo AF: 0.941

Asia WGS AF: 0.979 AC: 3406 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.3
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2102860; hg19: chr3-187110983;