rs9322676

Positions:

• chr6-102817684-G-A
• chr6-102817684-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.153 in 151,626 control chromosomes in the GnomAD database, including 4,416 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 0.15 (4416 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.189

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.444 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.153 AC: 23150 AN: 151508 Hom.: 4383 Cov.: 31

Gnomad AFR AF: 0.449

Gnomad AMI AF: 0.0285

Gnomad AMR AF: 0.101

Gnomad ASJ AF: 0.0326

Gnomad EAS AF: 0.0962

Gnomad SAS AF: 0.108

Gnomad FIN AF: 0.0269

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0214

Gnomad OTH AF: 0.111

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

GnomAD4 genome AF: 0.153 AC: 23252 AN: 151626 Hom.: 4416 Cov.: 31 AF XY: 0.150 AC XY: 11122 AN XY: 74130

Gnomad4 AFR AF: 0.450

Gnomad4 AMR AF: 0.102

Gnomad4 ASJ AF: 0.0326

Gnomad4 EAS AF: 0.0966

Gnomad4 SAS AF: 0.109

Gnomad4 FIN AF: 0.0269

Gnomad4 NFE AF: 0.0214

Gnomad4 OTH AF: 0.112

Alfa AF: 0.0145 Hom.: 14

Bravo AF: 0.174

Asia WGS AF: 0.144 AC: 499 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.6
DANN	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9322676; hg19: chr6-103265559;