rs7585700

Variant names:

• chr2-6364652-T-A
• rs7585700

Your query was ambiguous. Multiple possible variants found:

• chr2-6364652-T-A
• chr2-6364652-T-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 0.54 in 151,920 control chromosomes in the GnomAD database, including 22,676 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 0.54 (22676 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0110
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.653 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.540 AC: 82032 AN: 151802 Hom.: 22650 Cov.: 31

Gnomad AFR AF: 0.621

Gnomad AMI AF: 0.344

Gnomad AMR AF: 0.567

Gnomad ASJ AF: 0.518

Gnomad EAS AF: 0.671

Gnomad SAS AF: 0.501

Gnomad FIN AF: 0.531

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.484

Gnomad OTH AF: 0.534

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

GnomAD4 genome AF: 0.540 AC: 82109 AN: 151920 Hom.: 22676 Cov.: 31 AF XY: 0.545 AC XY: 40495 AN XY: 74246

African (AFR) AF: 0.621 AC: 25685 AN: 41390

American (AMR) AF: 0.568 AC: 8666 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.518 AC: 1798 AN: 3468

East Asian (EAS) AF: 0.671 AC: 3469 AN: 5168

South Asian (SAS) AF: 0.503 AC: 2424 AN: 4820

European-Finnish (FIN) AF: 0.531 AC: 5608 AN: 10552

Middle Eastern (MID) AF: 0.558 AC: 164 AN: 294

European-Non Finnish (NFE) AF: 0.484 AC: 32864 AN: 67952

Other (OTH) AF: 0.530 AC: 1118 AN: 2110

Alfa AF: 0.514 Hom.: 2583

Bravo AF: 0.547

Asia WGS AF: 0.554 AC: 1921 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	6.7
DANN	Benign	0.85
PhyloP100		-0.011

Splicing

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

Other links and lift over

dbSNP: rs7585700; hg19: chr2-6504784;