3-149128303-T-G

Variant names:

• chr3-149128303-T-G
• rs6805170

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 0.128 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.221

Gnomad4 AMR AF: 0.0936

Gnomad4 ASJ AF: 0.132

Gnomad4 EAS AF: 0.0961

Gnomad4 SAS AF: 0.0689

Gnomad4 FIN AF: 0.101

Gnomad4 NFE AF: 0.0903

Gnomad4 OTH AF: 0.116

Alfa AF: 0.0982 Hom.: 759

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6805170; hg19: chr3-148846090;