rs9322677

Variant names:

• chr6-102819005-A-G
• rs9322677

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 0.153 in 151,578 control chromosomes in the GnomAD database, including 4,426 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 (4426 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.957
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.153 AC: 23140 AN: 151460 Hom.: 4393 Cov.: 32

Gnomad AFR AF: 0.449

Gnomad AMI AF: 0.0285

Gnomad AMR AF: 0.101

Gnomad ASJ AF: 0.0323

Gnomad EAS AF: 0.0966

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.0267

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: 23242 AN: 151578 Hom.: 4426 Cov.: 32 AF XY: 0.150 AC XY: 11110 AN XY: 74076

African (AFR) AF: 0.449 AC: 18564 AN: 41314

American (AMR) AF: 0.102 AC: 1549 AN: 15204

Ashkenazi Jewish (ASJ) AF: 0.0323 AC: 112 AN: 3468

East Asian (EAS) AF: 0.0970 AC: 500 AN: 5152

South Asian (SAS) AF: 0.109 AC: 522 AN: 4800

European-Finnish (FIN) AF: 0.0267 AC: 281 AN: 10532

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0214 AC: 1448 AN: 67808

Other (OTH) AF: 0.112 AC: 234 AN: 2094

Alfa AF: 0.114 Hom.: 402

Bravo AF: 0.174

Asia WGS AF: 0.145 AC: 505 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.095
DANN	Benign	0.37
PhyloP100		-0.96

Splicing

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

Other links and lift over

dbSNP: rs9322677; hg19: chr6-103266880;