rs130624

Variant names:

• chr22-37042611-G-T
• rs130624

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 0.474 in 150,774 control chromosomes in the GnomAD database, including 19,749 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 0.47 (19749 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.849
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.643 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: 0.474 AC: 71407 AN: 150678 Hom.: 19736 Cov.: 31

Gnomad AFR AF: 0.180

Gnomad AMI AF: 0.605

Gnomad AMR AF: 0.653

Gnomad ASJ AF: 0.541

Gnomad EAS AF: 0.544

Gnomad SAS AF: 0.636

Gnomad FIN AF: 0.542

Gnomad MID AF: 0.610

Gnomad NFE AF: 0.575

Gnomad OTH AF: 0.522

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

GnomAD4 genome AF: 0.474 AC: 71438 AN: 150774 Hom.: 19749 Cov.: 31 AF XY: 0.481 AC XY: 35356 AN XY: 73580

African (AFR) AF: 0.180 AC: 7316 AN: 40702

American (AMR) AF: 0.653 AC: 9923 AN: 15190

Ashkenazi Jewish (ASJ) AF: 0.541 AC: 1876 AN: 3470

East Asian (EAS) AF: 0.544 AC: 2795 AN: 5138

South Asian (SAS) AF: 0.636 AC: 3058 AN: 4806

European-Finnish (FIN) AF: 0.542 AC: 5569 AN: 10284

Middle Eastern (MID) AF: 0.609 AC: 173 AN: 284

European-Non Finnish (NFE) AF: 0.576 AC: 39080 AN: 67904

Other (OTH) AF: 0.526 AC: 1097 AN: 2086

Alfa AF: 0.513 Hom.: 14617

Bravo AF: 0.466

Asia WGS AF: 0.610 AC: 2121 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.2
DANN	Benign	0.59
PhyloP100		0.85

Splicing

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

Other links and lift over

dbSNP: rs130624; hg19: chr22-37438651;