rs7024926

Variant names:

• chr9-80961357-A-C
• rs7024926

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 0.443 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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.965
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.243 AC: 10091 AN: 41496

American (AMR) AF: 0.434 AC: 6629 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.453 AC: 1573 AN: 3472

East Asian (EAS) AF: 0.238 AC: 1225 AN: 5152

South Asian (SAS) AF: 0.345 AC: 1666 AN: 4824

European-Finnish (FIN) AF: 0.585 AC: 6177 AN: 10562

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.564 AC: 38336 AN: 67950

Other (OTH) AF: 0.425 AC: 892 AN: 2100

Alfa AF: 0.531 Hom.: 12167

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
PhyloP100		-0.96

Splicing

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

Other links and lift over

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