rs9360921

Variant names:

• chr6-75555926-T-G
• rs9360921

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 0.108 in 152,076 control chromosomes in the GnomAD database, including 951 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 0.11 (951 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.22

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.12 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: 0.108 AC: 16461 AN: 151958 Hom.: 949 Cov.: 32

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.0931

Gnomad ASJ AF: 0.0942

Gnomad EAS AF: 0.0395

Gnomad SAS AF: 0.102

Gnomad FIN AF: 0.128

Gnomad MID AF: 0.102

Gnomad NFE AF: 0.106

Gnomad OTH AF: 0.105

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

GnomAD4 genome AF: 0.108 AC: 16477 AN: 152076 Hom.: 951 Cov.: 32 AF XY: 0.108 AC XY: 8038 AN XY: 74324

Gnomad4 AFR AF: 0.123

Gnomad4 AMR AF: 0.0931

Gnomad4 ASJ AF: 0.0942

Gnomad4 EAS AF: 0.0398

Gnomad4 SAS AF: 0.103

Gnomad4 FIN AF: 0.128

Gnomad4 NFE AF: 0.106

Gnomad4 OTH AF: 0.104

Alfa AF: 0.100 Hom.: 1465

Bravo AF: 0.104

Asia WGS AF: 0.0730 AC: 255 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	13
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9360921; hg19: chr6-76265642;