3-187661967-G-T

Variant names:

• chr3-187661967-G-T
• rs3864101

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 0.265 in 152,170 control chromosomes in the GnomAD database, including 5,975 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 0.27 (5975 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.91
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.397 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: 0.265 AC: 40329 AN: 152054 Hom.: 5953 Cov.: 33

Gnomad AFR AF: 0.401

Gnomad AMI AF: 0.177

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.191

Gnomad EAS AF: 0.211

Gnomad SAS AF: 0.178

Gnomad FIN AF: 0.215

Gnomad MID AF: 0.153

Gnomad NFE AF: 0.221

Gnomad OTH AF: 0.253

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

GnomAD4 genome AF: 0.265 AC: 40399 AN: 152170 Hom.: 5975 Cov.: 33 AF XY: 0.263 AC XY: 19580 AN XY: 74420

African (AFR) AF: 0.402 AC: 16686 AN: 41502

American (AMR) AF: 0.199 AC: 3036 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.191 AC: 662 AN: 3470

East Asian (EAS) AF: 0.212 AC: 1096 AN: 5182

South Asian (SAS) AF: 0.177 AC: 855 AN: 4818

European-Finnish (FIN) AF: 0.215 AC: 2281 AN: 10608

Middle Eastern (MID) AF: 0.158 AC: 46 AN: 292

European-Non Finnish (NFE) AF: 0.221 AC: 15038 AN: 67984

Other (OTH) AF: 0.255 AC: 538 AN: 2108

Alfa AF: 0.238 Hom.: 8876

Bravo AF: 0.268

Asia WGS AF: 0.218 AC: 757 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.10
DANN	Benign	0.37
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs3864101; hg19: chr3-187379755;