3-39548472-A-G

Position:

• chr3-39548472-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 0.618 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.619 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

Gnomad4 AFR AF: 0.274

Gnomad4 AMR AF: 0.681

Gnomad4 ASJ AF: 0.720

Gnomad4 EAS AF: 0.659

Gnomad4 SAS AF: 0.689

Gnomad4 FIN AF: 0.795

Gnomad4 NFE AF: 0.768

Gnomad4 OTH AF: 0.639

Alfa AF: 0.696 Hom.: 13510

Bravo AF: 0.594

Asia WGS AF: 0.639 AC: 2223 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11129837; hg19: chr3-39589963;