rs2687964

Variant names:

• chr4-39494652-G-T
• rs2687964

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 0.148 in 150,322 control chromosomes in the GnomAD database, including 1,899 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 0.15 (1899 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.675
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.184 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: 0.148 AC: 22183 AN: 150226 Hom.: 1898 Cov.: 30

Gnomad AFR AF: 0.0719

Gnomad AMI AF: 0.221

Gnomad AMR AF: 0.156

Gnomad ASJ AF: 0.207

Gnomad EAS AF: 0.124

Gnomad SAS AF: 0.176

Gnomad FIN AF: 0.141

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.187

Gnomad OTH AF: 0.187

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

GnomAD4 genome AF: 0.148 AC: 22176 AN: 150322 Hom.: 1899 Cov.: 30 AF XY: 0.144 AC XY: 10555 AN XY: 73214

African (AFR) AF: 0.0717 AC: 2938 AN: 40948

American (AMR) AF: 0.156 AC: 2340 AN: 14982

Ashkenazi Jewish (ASJ) AF: 0.207 AC: 717 AN: 3462

East Asian (EAS) AF: 0.124 AC: 639 AN: 5134

South Asian (SAS) AF: 0.176 AC: 835 AN: 4742

European-Finnish (FIN) AF: 0.141 AC: 1407 AN: 9998

Middle Eastern (MID) AF: 0.240 AC: 70 AN: 292

European-Non Finnish (NFE) AF: 0.187 AC: 12641 AN: 67776

Other (OTH) AF: 0.187 AC: 389 AN: 2084

Alfa AF: 0.174 Hom.: 6291

Bravo AF: 0.146

Asia WGS AF: 0.148 AC: 516 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	11
DANN	Benign	0.75
PhyloP100		0.68

Splicing

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

Other links and lift over

dbSNP: rs2687964; hg19: chr4-39496272;