rs7652589

Positions:

• chr3-122170241-A-G

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 0.598 in 152,010 control chromosomes in the GnomAD database, including 27,534 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 0.60 (27534 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.980

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.718 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.598 AC: 90792 AN: 151892 Hom.: 27506 Cov.: 31

Gnomad AFR AF: 0.592

Gnomad AMI AF: 0.627

Gnomad AMR AF: 0.728

Gnomad ASJ AF: 0.619

Gnomad EAS AF: 0.370

Gnomad SAS AF: 0.465

Gnomad FIN AF: 0.516

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.609

Gnomad OTH AF: 0.621

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

GnomAD4 genome AF: 0.598 AC: 90869 AN: 152010 Hom.: 27534 Cov.: 31 AF XY: 0.596 AC XY: 44276 AN XY: 74282

Gnomad4 AFR AF: 0.593

Gnomad4 AMR AF: 0.729

Gnomad4 ASJ AF: 0.619

Gnomad4 EAS AF: 0.371

Gnomad4 SAS AF: 0.465

Gnomad4 FIN AF: 0.516

Gnomad4 NFE AF: 0.609

Gnomad4 OTH AF: 0.616

Alfa AF: 0.618 Hom.: 38153

Bravo AF: 0.617

Asia WGS AF: 0.395 AC: 1375 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	2.1
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7652589; hg19: chr3-121889088;