rs9320781

Variant names:

• chr6-120955581-A-C
• rs9320781

Your query was ambiguous. Multiple possible variants found:

• chr6-120955581-A-C
• chr6-120955581-A-G

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 0.146 in 152,200 control chromosomes in the GnomAD database, including 2,546 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 (2546 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.925
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.581 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: 0.146 AC: 22252 AN: 152082 Hom.: 2541 Cov.: 32

Gnomad AFR AF: 0.0503

Gnomad AMI AF: 0.133

Gnomad AMR AF: 0.146

Gnomad ASJ AF: 0.244

Gnomad EAS AF: 0.600

Gnomad SAS AF: 0.322

Gnomad FIN AF: 0.200

Gnomad MID AF: 0.274

Gnomad NFE AF: 0.143

Gnomad OTH AF: 0.170

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

GnomAD4 genome AF: 0.146 AC: 22277 AN: 152200 Hom.: 2546 Cov.: 32 AF XY: 0.153 AC XY: 11370 AN XY: 74414

African (AFR) AF: 0.0503 AC: 2092 AN: 41576

American (AMR) AF: 0.147 AC: 2245 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.244 AC: 846 AN: 3470

East Asian (EAS) AF: 0.599 AC: 3092 AN: 5162

South Asian (SAS) AF: 0.324 AC: 1561 AN: 4818

European-Finnish (FIN) AF: 0.200 AC: 2119 AN: 10580

Middle Eastern (MID) AF: 0.277 AC: 81 AN: 292

European-Non Finnish (NFE) AF: 0.143 AC: 9753 AN: 67994

Other (OTH) AF: 0.174 AC: 367 AN: 2110

Alfa AF: 0.111 Hom.: 518

Bravo AF: 0.137

Asia WGS AF: 0.416 AC: 1445 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	7.7
DANN	Benign	0.88
PhyloP100		0.93

Splicing

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

Other links and lift over

dbSNP: rs9320781; hg19: chr6-121276727;