rs9360664

Variant names:

• chr6-73331701-G-A
• rs9360664

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 0.138 in 152,116 control chromosomes in the GnomAD database, including 1,722 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 0.14 (1722 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.561
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.197 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: 0.138 AC: 20981 AN: 151998 Hom.: 1723 Cov.: 32

Gnomad AFR AF: 0.0475

Gnomad AMI AF: 0.221

Gnomad AMR AF: 0.128

Gnomad ASJ AF: 0.141

Gnomad EAS AF: 0.141

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.178

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.151

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

GnomAD4 genome AF: 0.138 AC: 20974 AN: 152116 Hom.: 1722 Cov.: 32 AF XY: 0.139 AC XY: 10328 AN XY: 74338

African (AFR) AF: 0.0474 AC: 1967 AN: 41502

American (AMR) AF: 0.127 AC: 1944 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.141 AC: 488 AN: 3470

East Asian (EAS) AF: 0.141 AC: 731 AN: 5194

South Asian (SAS) AF: 0.208 AC: 1003 AN: 4818

European-Finnish (FIN) AF: 0.178 AC: 1880 AN: 10560

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.182 AC: 12397 AN: 67986

Other (OTH) AF: 0.149 AC: 316 AN: 2114

Alfa AF: 0.171 Hom.: 3593

Bravo AF: 0.127

Asia WGS AF: 0.148 AC: 512 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.9
DANN	Benign	0.50
PhyloP100		0.56

Splicing

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

Other links and lift over

dbSNP: rs9360664; hg19: chr6-74041424;