chr3-39548472-A-G

Variant names:

• chr3-39548472-A-G
• rs11129837

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 0.618 in 152,026 control chromosomes in the GnomAD database, including 32,688 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 0.62 (32688 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.75
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.763 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: 0.619 AC: 93960 AN: 151908 Hom.: 32692 Cov.: 31

Gnomad AFR AF: 0.274

Gnomad AMI AF: 0.904

Gnomad AMR AF: 0.681

Gnomad ASJ AF: 0.720

Gnomad EAS AF: 0.659

Gnomad SAS AF: 0.688

Gnomad FIN AF: 0.795

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.768

Gnomad OTH AF: 0.639

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

GnomAD4 genome AF: 0.618 AC: 93966 AN: 152026 Hom.: 32688 Cov.: 31 AF XY: 0.622 AC XY: 46244 AN XY: 74298

African (AFR) AF: 0.274 AC: 11356 AN: 41442

American (AMR) AF: 0.681 AC: 10404 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.720 AC: 2499 AN: 3470

East Asian (EAS) AF: 0.659 AC: 3403 AN: 5164

South Asian (SAS) AF: 0.689 AC: 3321 AN: 4818

European-Finnish (FIN) AF: 0.795 AC: 8400 AN: 10566

Middle Eastern (MID) AF: 0.616 AC: 181 AN: 294

European-Non Finnish (NFE) AF: 0.768 AC: 52229 AN: 67978

Other (OTH) AF: 0.639 AC: 1350 AN: 2114

Alfa AF: 0.692 Hom.: 22543

Bravo AF: 0.594

Asia WGS AF: 0.639 AC: 2223 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.1
DANN	Benign	0.62
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs11129837; hg19: chr3-39589963;