9-80961357-A-C

Position:

• chr9-80961357-A-C

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 0.443 in 152,042 control chromosomes in the GnomAD database, including 16,588 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 0.44 (16588 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.965

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.559 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.80961357A>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.443 AC: 67357 AN: 151922 Hom.: 16589 Cov.: 32

Gnomad AFR AF: 0.243

Gnomad AMI AF: 0.723

Gnomad AMR AF: 0.434

Gnomad ASJ AF: 0.453

Gnomad EAS AF: 0.237

Gnomad SAS AF: 0.344

Gnomad FIN AF: 0.585

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.564

Gnomad OTH AF: 0.427

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

GnomAD4 genome AF: 0.443 AC: 67380 AN: 152042 Hom.: 16588 Cov.: 32 AF XY: 0.441 AC XY: 32765 AN XY: 74326

Gnomad4 AFR AF: 0.243

Gnomad4 AMR AF: 0.434

Gnomad4 ASJ AF: 0.453

Gnomad4 EAS AF: 0.238

Gnomad4 SAS AF: 0.345

Gnomad4 FIN AF: 0.585

Gnomad4 NFE AF: 0.564

Gnomad4 OTH AF: 0.425

Alfa AF: 0.530 Hom.: 11025

Bravo AF: 0.425

Asia WGS AF: 0.299 AC: 1042 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.2
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7024926; hg19: chr9-83576272; COSMIC: COSV60366345;