rs9502979

Variant names:

• chr6-213983-G-T
• rs9502979

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 0.0704 in 152,202 control chromosomes in the GnomAD database, including 1,038 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 0.070 (1038 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.41 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: 0.0702 AC: 10682 AN: 152084 Hom.: 1033 Cov.: 33

Gnomad AFR AF: 0.138

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.0118

Gnomad EAS AF: 0.423

Gnomad SAS AF: 0.0725

Gnomad FIN AF: 0.0213

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.00320

Gnomad OTH AF: 0.0583

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

GnomAD4 genome AF: 0.0704 AC: 10709 AN: 152202 Hom.: 1038 Cov.: 33 AF XY: 0.0742 AC XY: 5526 AN XY: 74436

African (AFR) AF: 0.138 AC: 5742 AN: 41506

American (AMR) AF: 0.119 AC: 1814 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0118 AC: 41 AN: 3470

East Asian (EAS) AF: 0.425 AC: 2196 AN: 5172

South Asian (SAS) AF: 0.0715 AC: 344 AN: 4812

European-Finnish (FIN) AF: 0.0213 AC: 226 AN: 10614

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.00322 AC: 219 AN: 68014

Other (OTH) AF: 0.0596 AC: 126 AN: 2114

Alfa AF: 0.0234 Hom.: 151

Bravo AF: 0.0814

Asia WGS AF: 0.206 AC: 717 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.9
DANN	Benign	0.73
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs9502979; hg19: chr6-213983;