6-9529786-C-T

Variant names:

• chr6-9529786-C-T
• rs1997770

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 0.934 in 151,490 control chromosomes in the GnomAD database, including 66,142 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 0.93 (66142 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.524
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.967 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: 0.934 AC: 141305 AN: 151354 Hom.: 66068 Cov.: 31

Gnomad AFR AF: 0.975

Gnomad AMI AF: 0.882

Gnomad AMR AF: 0.954

Gnomad ASJ AF: 0.911

Gnomad EAS AF: 0.974

Gnomad SAS AF: 0.928

Gnomad FIN AF: 0.908

Gnomad MID AF: 0.894

Gnomad NFE AF: 0.907

Gnomad OTH AF: 0.935

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

GnomAD4 genome AF: 0.934 AC: 141449 AN: 151490 Hom.: 66142 Cov.: 31 AF XY: 0.935 AC XY: 69236 AN XY: 74038

African (AFR) AF: 0.975 AC: 40470 AN: 41514

American (AMR) AF: 0.954 AC: 14547 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.911 AC: 3157 AN: 3466

East Asian (EAS) AF: 0.974 AC: 5016 AN: 5150

South Asian (SAS) AF: 0.928 AC: 4449 AN: 4794

European-Finnish (FIN) AF: 0.908 AC: 9551 AN: 10514

Middle Eastern (MID) AF: 0.908 AC: 187 AN: 206

European-Non Finnish (NFE) AF: 0.907 AC: 61318 AN: 67608

Other (OTH) AF: 0.936 AC: 1953 AN: 2086

Alfa AF: 0.914 Hom.: 128150

Bravo AF: 0.940

Asia WGS AF: 0.955 AC: 3252 AN: 3408

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.66
DANN	Benign	0.49
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs1997770; hg19: chr6-9530019;