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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.540 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

Gnomad4 AFR AF: 0.621

Gnomad4 AMR AF: 0.568

Gnomad4 ASJ AF: 0.518

Gnomad4 EAS AF: 0.671

Gnomad4 SAS AF: 0.503

Gnomad4 FIN AF: 0.531

Gnomad4 NFE AF: 0.484

Gnomad4 OTH AF: 0.530

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7585700; hg19: chr2-6504784;