rs9321807

Variant names:

• chr6-141281542-A-G
• rs9321807

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 0.0828 in 152,166 control chromosomes in the GnomAD database, including 804 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 0.083 (804 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.95

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 (SAS) allele frequency at 95% confidence interval = 0.176 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: 0.0827 AC: 12569 AN: 152048 Hom.: 800 Cov.: 32

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.0570

Gnomad AMR AF: 0.0483

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.176

Gnomad SAS AF: 0.186

Gnomad FIN AF: 0.0331

Gnomad MID AF: 0.0924

Gnomad NFE AF: 0.0379

Gnomad OTH AF: 0.0870

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

GnomAD4 genome AF: 0.0828 AC: 12595 AN: 152166 Hom.: 804 Cov.: 32 AF XY: 0.0849 AC XY: 6319 AN XY: 74390

Gnomad4 AFR AF: 0.154

Gnomad4 AMR AF: 0.0483

Gnomad4 ASJ AF: 0.134

Gnomad4 EAS AF: 0.176

Gnomad4 SAS AF: 0.186

Gnomad4 FIN AF: 0.0331

Gnomad4 NFE AF: 0.0379

Gnomad4 OTH AF: 0.0932

Alfa AF: 0.0490 Hom.: 336

Bravo AF: 0.0842

Asia WGS AF: 0.200 AC: 696 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	2.7
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9321807; hg19: chr6-141602679;