rs9360664

Positions:

• chr6-73331701-G-A

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 0.138 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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.561

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
		n.73331701G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.0474

Gnomad4 AMR AF: 0.127

Gnomad4 ASJ AF: 0.141

Gnomad4 EAS AF: 0.141

Gnomad4 SAS AF: 0.208

Gnomad4 FIN AF: 0.178

Gnomad4 NFE AF: 0.182

Gnomad4 OTH AF: 0.149

Alfa AF: 0.172 Hom.: 2993

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9360664; hg19: chr6-74041424;