6-160685089-C-T

Variant names:

• chr6-160685089-C-T
• rs9347440

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 0.533 in 150,230 control chromosomes in the GnomAD database, including 21,350 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 0.53 (21350 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0760
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.59 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: 0.533 AC: 80046 AN: 150112 Hom.: 21322 Cov.: 32

Gnomad AFR AF: 0.596

Gnomad AMI AF: 0.511

Gnomad AMR AF: 0.430

Gnomad ASJ AF: 0.548

Gnomad EAS AF: 0.358

Gnomad SAS AF: 0.372

Gnomad FIN AF: 0.595

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.533

Gnomad OTH AF: 0.554

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

GnomAD4 genome AF: 0.533 AC: 80119 AN: 150230 Hom.: 21350 Cov.: 32 AF XY: 0.529 AC XY: 38861 AN XY: 73454

African (AFR) AF: 0.596 AC: 24247 AN: 40682

American (AMR) AF: 0.429 AC: 6521 AN: 15190

Ashkenazi Jewish (ASJ) AF: 0.548 AC: 1889 AN: 3444

East Asian (EAS) AF: 0.358 AC: 1838 AN: 5140

South Asian (SAS) AF: 0.370 AC: 1770 AN: 4782

European-Finnish (FIN) AF: 0.595 AC: 6188 AN: 10392

Middle Eastern (MID) AF: 0.625 AC: 180 AN: 288

European-Non Finnish (NFE) AF: 0.533 AC: 35862 AN: 67322

Other (OTH) AF: 0.557 AC: 1160 AN: 2082

Alfa AF: 0.338 Hom.: 621

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	8.1
DANN	Benign	0.85
PhyloP100		0.076

Splicing

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

Other links and lift over

dbSNP: rs9347440; hg19: chr6-161106121;