chr3-166241576-G-A

Position:

• chr3-166241576-G-A

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 0.716 in 151,522 control chromosomes in the GnomAD database, including 39,045 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 0.72 (39045 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.762 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: 0.716 AC: 108440 AN: 151404 Hom.: 39005 Cov.: 31

Gnomad AFR AF: 0.766

Gnomad AMI AF: 0.496

Gnomad AMR AF: 0.674

Gnomad ASJ AF: 0.634

Gnomad EAS AF: 0.690

Gnomad SAS AF: 0.782

Gnomad FIN AF: 0.807

Gnomad MID AF: 0.643

Gnomad NFE AF: 0.687

Gnomad OTH AF: 0.684

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

GnomAD4 genome AF: 0.716 AC: 108540 AN: 151522 Hom.: 39045 Cov.: 31 AF XY: 0.723 AC XY: 53481 AN XY: 73994

Gnomad4 AFR AF: 0.766

Gnomad4 AMR AF: 0.673

Gnomad4 ASJ AF: 0.634

Gnomad4 EAS AF: 0.690

Gnomad4 SAS AF: 0.782

Gnomad4 FIN AF: 0.807

Gnomad4 NFE AF: 0.687

Gnomad4 OTH AF: 0.683

Alfa AF: 0.712 Hom.: 4816

Bravo AF: 0.705

Asia WGS AF: 0.741 AC: 2570 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.064
DANN	Benign	0.17

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1530207; hg19: chr3-165959364;