rs7577642

chr2-85472627-C-T

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 0.713 in 152,082 control chromosomes in the GnomAD database, including 39,018 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 0.71 (39018 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.307

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.862 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.713 AC: 108357 AN: 151964 Hom.: 38995 Cov.: 32

Gnomad AFR AF: 0.618

Gnomad AMI AF: 0.887

Gnomad AMR AF: 0.745

Gnomad ASJ AF: 0.748

Gnomad EAS AF: 0.882

Gnomad SAS AF: 0.862

Gnomad FIN AF: 0.738

Gnomad MID AF: 0.794

Gnomad NFE AF: 0.731

Gnomad OTH AF: 0.739

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

GnomAD4 genome AF: 0.713 AC: 108422 AN: 152082 Hom.: 39018 Cov.: 32 AF XY: 0.716 AC XY: 53200 AN XY: 74328

Gnomad4 AFR AF: 0.618

Gnomad4 AMR AF: 0.745

Gnomad4 ASJ AF: 0.748

Gnomad4 EAS AF: 0.883

Gnomad4 SAS AF: 0.862

Gnomad4 FIN AF: 0.738

Gnomad4 NFE AF: 0.731

Gnomad4 OTH AF: 0.740

Alfa AF: 0.734 Hom.: 96017

Bravo AF: 0.710

Asia WGS AF: 0.865 AC: 3003 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	1.2
Dann	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7577642; hg19: chr2-85699750;