rs9275313

Variant names:

• chr6-32697982-G-T
• rs9275313

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 0.1 in 139,408 control chromosomes in the GnomAD database, including 821 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 0.10 (821 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.334
• Publications: 17 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.188 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: 0.100 AC: 13960 AN: 139296 Hom.: 820 Cov.: 30

Gnomad AFR AF: 0.0406

Gnomad AMI AF: 0.151

Gnomad AMR AF: 0.194

Gnomad ASJ AF: 0.190

Gnomad EAS AF: 0.0877

Gnomad SAS AF: 0.0892

Gnomad FIN AF: 0.115

Gnomad MID AF: 0.106

Gnomad NFE AF: 0.109

Gnomad OTH AF: 0.101

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

GnomAD4 genome AF: 0.100 AC: 13980 AN: 139408 Hom.: 821 Cov.: 30 AF XY: 0.102 AC XY: 6973 AN XY: 68048

African (AFR) AF: 0.0408 AC: 1543 AN: 37800

American (AMR) AF: 0.194 AC: 2756 AN: 14206

Ashkenazi Jewish (ASJ) AF: 0.190 AC: 588 AN: 3090

East Asian (EAS) AF: 0.0881 AC: 395 AN: 4482

South Asian (SAS) AF: 0.0890 AC: 327 AN: 3674

European-Finnish (FIN) AF: 0.115 AC: 1175 AN: 10236

Middle Eastern (MID) AF: 0.107 AC: 29 AN: 272

European-Non Finnish (NFE) AF: 0.109 AC: 6844 AN: 62860

Other (OTH) AF: 0.100 AC: 193 AN: 1928

Alfa AF: 0.106 Hom.: 1783

Bravo AF: 0.0987

Asia WGS AF: 0.0600 AC: 211 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	7.4
DANN	Benign	0.64
PhyloP100		0.33

Splicing

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

Other links and lift over

dbSNP: rs9275313; hg19: chr6-32665759;