6-159852667-G-T

Variant names:

• chr6-159852667-G-T
• rs9457743

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 0.638 in 152,006 control chromosomes in the GnomAD database, including 31,320 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 0.64 (31320 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.70

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.675 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: 0.638 AC: 96967 AN: 151888 Hom.: 31313 Cov.: 31

Gnomad AFR AF: 0.633

Gnomad AMI AF: 0.555

Gnomad AMR AF: 0.598

Gnomad ASJ AF: 0.668

Gnomad EAS AF: 0.341

Gnomad SAS AF: 0.647

Gnomad FIN AF: 0.582

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.680

Gnomad OTH AF: 0.663

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

GnomAD4 genome AF: 0.638 AC: 97002 AN: 152006 Hom.: 31320 Cov.: 31 AF XY: 0.630 AC XY: 46825 AN XY: 74288

Gnomad4 AFR AF: 0.633

Gnomad4 AMR AF: 0.598

Gnomad4 ASJ AF: 0.668

Gnomad4 EAS AF: 0.341

Gnomad4 SAS AF: 0.647

Gnomad4 FIN AF: 0.582

Gnomad4 NFE AF: 0.680

Gnomad4 OTH AF: 0.657

Alfa AF: 0.652 Hom.: 13263

Bravo AF: 0.637

Asia WGS AF: 0.486 AC: 1695 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.26
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9457743; hg19: chr6-160273699;