rs2087017

Variant names:

• chr3-114123166-G-A
• rs2087017

Your query was ambiguous. Multiple possible variants found:

• chr3-114123166-G-A
• chr3-114123166-G-C

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 0.528 in 151,792 control chromosomes in the GnomAD database, including 21,340 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 0.53 (21340 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.338
• Publications: 18 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 (AMR) allele frequency at 95% confidence interval = 0.594 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: 0.528 AC: 80150 AN: 151678 Hom.: 21332 Cov.: 31

Gnomad AFR AF: 0.443

Gnomad AMI AF: 0.522

Gnomad AMR AF: 0.604

Gnomad ASJ AF: 0.626

Gnomad EAS AF: 0.488

Gnomad SAS AF: 0.545

Gnomad FIN AF: 0.571

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.552

Gnomad OTH AF: 0.566

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

GnomAD4 genome AF: 0.528 AC: 80189 AN: 151792 Hom.: 21340 Cov.: 31 AF XY: 0.534 AC XY: 39582 AN XY: 74140

African (AFR) AF: 0.443 AC: 18319 AN: 41384

American (AMR) AF: 0.605 AC: 9220 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.626 AC: 2171 AN: 3468

East Asian (EAS) AF: 0.488 AC: 2521 AN: 5164

South Asian (SAS) AF: 0.545 AC: 2615 AN: 4796

European-Finnish (FIN) AF: 0.571 AC: 5985 AN: 10480

Middle Eastern (MID) AF: 0.656 AC: 193 AN: 294

European-Non Finnish (NFE) AF: 0.552 AC: 37508 AN: 67934

Other (OTH) AF: 0.560 AC: 1183 AN: 2112

Alfa AF: 0.546 Hom.: 65605

Bravo AF: 0.527

Asia WGS AF: 0.497 AC: 1727 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	0.90
DANN	Benign	0.33
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs2087017; hg19: chr3-113842013;