rs9395767

Variant names:

• chr6-52181972-T-A
• rs9395767

Your query was ambiguous. Multiple possible variants found:

• chr6-52181972-T-A
• chr6-52181972-T-C

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 0.449 in 152,126 control chromosomes in the GnomAD database, including 18,301 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 0.45 (18301 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.32
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.61 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: 0.450 AC: 68377 AN: 152008 Hom.: 18302 Cov.: 33

Gnomad AFR AF: 0.189

Gnomad AMI AF: 0.519

Gnomad AMR AF: 0.408

Gnomad ASJ AF: 0.625

Gnomad EAS AF: 0.175

Gnomad SAS AF: 0.394

Gnomad FIN AF: 0.553

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.615

Gnomad OTH AF: 0.506

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

GnomAD4 genome AF: 0.449 AC: 68375 AN: 152126 Hom.: 18301 Cov.: 33 AF XY: 0.444 AC XY: 32988 AN XY: 74370

African (AFR) AF: 0.188 AC: 7821 AN: 41492

American (AMR) AF: 0.407 AC: 6219 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.625 AC: 2165 AN: 3464

East Asian (EAS) AF: 0.176 AC: 907 AN: 5168

South Asian (SAS) AF: 0.394 AC: 1899 AN: 4814

European-Finnish (FIN) AF: 0.553 AC: 5858 AN: 10592

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.615 AC: 41815 AN: 67998

Other (OTH) AF: 0.502 AC: 1061 AN: 2114

Alfa AF: 0.397 Hom.: 1282

Bravo AF: 0.426

Asia WGS AF: 0.305 AC: 1062 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.035
DANN	Benign	0.64
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs9395767; hg19: chr6-52046770;