3-148642259-T-G

Variant names:

• chr3-148642259-T-G
• rs9811115

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 0.553 in 151,788 control chromosomes in the GnomAD database, including 24,725 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 0.55 (24725 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.346
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.783 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.554 AC: 83955 AN: 151670 Hom.: 24706 Cov.: 30

Gnomad AFR AF: 0.360

Gnomad AMI AF: 0.498

Gnomad AMR AF: 0.690

Gnomad ASJ AF: 0.503

Gnomad EAS AF: 0.804

Gnomad SAS AF: 0.535

Gnomad FIN AF: 0.693

Gnomad MID AF: 0.433

Gnomad NFE AF: 0.605

Gnomad OTH AF: 0.558

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

GnomAD4 genome AF: 0.553 AC: 84014 AN: 151788 Hom.: 24725 Cov.: 30 AF XY: 0.560 AC XY: 41518 AN XY: 74156

African (AFR) AF: 0.360 AC: 14888 AN: 41364

American (AMR) AF: 0.691 AC: 10511 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.503 AC: 1741 AN: 3462

East Asian (EAS) AF: 0.803 AC: 4126 AN: 5136

South Asian (SAS) AF: 0.537 AC: 2582 AN: 4810

European-Finnish (FIN) AF: 0.693 AC: 7306 AN: 10542

Middle Eastern (MID) AF: 0.445 AC: 130 AN: 292

European-Non Finnish (NFE) AF: 0.605 AC: 41108 AN: 67948

Other (OTH) AF: 0.555 AC: 1170 AN: 2108

Alfa AF: 0.574 Hom.: 4569

Bravo AF: 0.552

Asia WGS AF: 0.646 AC: 2246 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.3
DANN	Benign	0.42
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs9811115; hg19: chr3-148360046;