rs2102860

Positions:

• 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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.539

Genes affected

(HGNC:):

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/exons	MANE	Protein	UniProt
		n.187393195G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;