3-148617243-C-T

Variant names:

• chr3-148617243-C-T
• rs6803324

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 0.0692 in 152,126 control chromosomes in the GnomAD database, including 685 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 0.069 (685 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.136
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.195 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: 0.0688 AC: 10461 AN: 152008 Hom.: 666 Cov.: 32

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.0669

Gnomad AMR AF: 0.134

Gnomad ASJ AF: 0.0481

Gnomad EAS AF: 0.204

Gnomad SAS AF: 0.0496

Gnomad FIN AF: 0.0609

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0131

Gnomad OTH AF: 0.0708

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

GnomAD4 genome AF: 0.0692 AC: 10533 AN: 152126 Hom.: 685 Cov.: 32 AF XY: 0.0729 AC XY: 5417 AN XY: 74356

African (AFR) AF: 0.126 AC: 5240 AN: 41476

American (AMR) AF: 0.135 AC: 2062 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0481 AC: 167 AN: 3472

East Asian (EAS) AF: 0.205 AC: 1059 AN: 5164

South Asian (SAS) AF: 0.0498 AC: 240 AN: 4818

European-Finnish (FIN) AF: 0.0609 AC: 645 AN: 10586

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0132 AC: 895 AN: 68016

Other (OTH) AF: 0.0715 AC: 151 AN: 2112

Alfa AF: 0.0349 Hom.: 1134

Bravo AF: 0.0792

Asia WGS AF: 0.103 AC: 356 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.9
DANN	Benign	0.54
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs6803324; hg19: chr3-148335030;