3-149128303-T-G

Variant names:

• chr3-149128303-T-G
• rs6805170

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 0.128 in 152,222 control chromosomes in the GnomAD database, including 1,495 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 0.13 (1495 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.100
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.217 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: 0.128 AC: 19428 AN: 152104 Hom.: 1495 Cov.: 33

Gnomad AFR AF: 0.221

Gnomad AMI AF: 0.0780

Gnomad AMR AF: 0.0937

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.0963

Gnomad SAS AF: 0.0678

Gnomad FIN AF: 0.101

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0903

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.128 AC: 19436 AN: 152222 Hom.: 1495 Cov.: 33 AF XY: 0.127 AC XY: 9435 AN XY: 74438

African (AFR) AF: 0.221 AC: 9162 AN: 41514

American (AMR) AF: 0.0936 AC: 1432 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.132 AC: 459 AN: 3470

East Asian (EAS) AF: 0.0961 AC: 498 AN: 5182

South Asian (SAS) AF: 0.0689 AC: 332 AN: 4816

European-Finnish (FIN) AF: 0.101 AC: 1066 AN: 10602

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.0903 AC: 6141 AN: 68026

Other (OTH) AF: 0.116 AC: 244 AN: 2108

Alfa AF: 0.102 Hom.: 1120

Bravo AF: 0.132

Asia WGS AF: 0.100 AC: 349 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.2
DANN	Benign	0.67
PhyloP100		-0.10

Splicing

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

Other links and lift over

dbSNP: rs6805170; hg19: chr3-148846090;