rs2714594

Variant names:

• chr7-67698718-G-A
• rs2714594

Your query was ambiguous. Multiple possible variants found:

• chr7-67698718-G-A
• chr7-67698718-G-C
• chr7-67698718-G-T

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 0.402 in 151,954 control chromosomes in the GnomAD database, including 12,435 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 0.40 (12435 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365
• Publications: 2 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 (EAS) allele frequency at 95% confidence interval = 0.414 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.402 AC: 60976 AN: 151836 Hom.: 12425 Cov.: 32

Gnomad AFR AF: 0.411

Gnomad AMI AF: 0.399

Gnomad AMR AF: 0.303

Gnomad ASJ AF: 0.310

Gnomad EAS AF: 0.419

Gnomad SAS AF: 0.325

Gnomad FIN AF: 0.464

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.418

Gnomad OTH AF: 0.378

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

GnomAD4 genome AF: 0.402 AC: 61020 AN: 151954 Hom.: 12435 Cov.: 32 AF XY: 0.402 AC XY: 29839 AN XY: 74258

African (AFR) AF: 0.411 AC: 17047 AN: 41456

American (AMR) AF: 0.302 AC: 4617 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.310 AC: 1077 AN: 3470

East Asian (EAS) AF: 0.419 AC: 2155 AN: 5142

South Asian (SAS) AF: 0.326 AC: 1572 AN: 4822

European-Finnish (FIN) AF: 0.464 AC: 4894 AN: 10544

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.418 AC: 28411 AN: 67942

Other (OTH) AF: 0.377 AC: 793 AN: 2104

Alfa AF: 0.319 Hom.: 1226

Bravo AF: 0.389

Asia WGS AF: 0.366 AC: 1271 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.8
DANN	Benign	0.42
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs2714594; hg19: chr7-67163705;