chr13-42524192-A-G

Variant names:

• chr13-42524192-A-G
• rs4942139

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 0.708 in 152,144 control chromosomes in the GnomAD database, including 38,432 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 (38432 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00500
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.786 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: 0.709 AC: 107719 AN: 152024 Hom.: 38415 Cov.: 33

Gnomad AFR AF: 0.664

Gnomad AMI AF: 0.742

Gnomad AMR AF: 0.798

Gnomad ASJ AF: 0.717

Gnomad EAS AF: 0.771

Gnomad SAS AF: 0.664

Gnomad FIN AF: 0.631

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.725

Gnomad OTH AF: 0.722

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

GnomAD4 genome AF: 0.708 AC: 107777 AN: 152144 Hom.: 38432 Cov.: 33 AF XY: 0.704 AC XY: 52353 AN XY: 74388

African (AFR) AF: 0.663 AC: 27500 AN: 41482

American (AMR) AF: 0.798 AC: 12205 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.717 AC: 2491 AN: 3472

East Asian (EAS) AF: 0.770 AC: 3994 AN: 5184

South Asian (SAS) AF: 0.664 AC: 3201 AN: 4820

European-Finnish (FIN) AF: 0.631 AC: 6681 AN: 10592

Middle Eastern (MID) AF: 0.646 AC: 190 AN: 294

European-Non Finnish (NFE) AF: 0.725 AC: 49323 AN: 67992

Other (OTH) AF: 0.720 AC: 1520 AN: 2112

Alfa AF: 0.716 Hom.: 4887

Bravo AF: 0.725

Asia WGS AF: 0.696 AC: 2417 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.4
DANN	Benign	0.63
PhyloP100		0.0050

Splicing

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

Other links and lift over

dbSNP: rs4942139; hg19: chr13-43098328;