chr3-122170241-A-G

Variant names:

• chr3-122170241-A-G
• rs7652589

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 0.598 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
• Publications: 24 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

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: 0.598 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

African (AFR) AF: 0.593 AC: 24557 AN: 41444

American (AMR) AF: 0.729 AC: 11134 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.619 AC: 2147 AN: 3470

East Asian (EAS) AF: 0.371 AC: 1917 AN: 5170

South Asian (SAS) AF: 0.465 AC: 2243 AN: 4820

European-Finnish (FIN) AF: 0.516 AC: 5440 AN: 10546

Middle Eastern (MID) AF: 0.653 AC: 192 AN: 294

European-Non Finnish (NFE) AF: 0.609 AC: 41370 AN: 67974

Other (OTH) AF: 0.616 AC: 1298 AN: 2108

Alfa AF: 0.619 Hom.: 48885

Bravo AF: 0.617

Asia WGS AF: 0.395 AC: 1375 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	2.1
DANN	Benign	0.46
PhyloP100		-0.98

Splicing

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

Other links and lift over

dbSNP: rs7652589; hg19: chr3-121889088;