9-7734250-G-A

Variant names:

• chr9-7734250-G-A
• rs10758892

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 0.898 in 152,068 control chromosomes in the GnomAD database, including 61,694 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 0.90 (61694 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.77
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.941 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: 0.898 AC: 136518 AN: 151950 Hom.: 61675 Cov.: 30

Gnomad AFR AF: 0.791

Gnomad AMI AF: 0.989

Gnomad AMR AF: 0.898

Gnomad ASJ AF: 0.912

Gnomad EAS AF: 0.925

Gnomad SAS AF: 0.920

Gnomad FIN AF: 0.974

Gnomad MID AF: 0.905

Gnomad NFE AF: 0.947

Gnomad OTH AF: 0.899

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

GnomAD4 genome AF: 0.898 AC: 136589 AN: 152068 Hom.: 61694 Cov.: 30 AF XY: 0.900 AC XY: 66911 AN XY: 74340

African (AFR) AF: 0.790 AC: 32753 AN: 41442

American (AMR) AF: 0.897 AC: 13681 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.912 AC: 3166 AN: 3472

East Asian (EAS) AF: 0.925 AC: 4777 AN: 5166

South Asian (SAS) AF: 0.920 AC: 4437 AN: 4822

European-Finnish (FIN) AF: 0.974 AC: 10327 AN: 10600

Middle Eastern (MID) AF: 0.898 AC: 264 AN: 294

European-Non Finnish (NFE) AF: 0.947 AC: 64389 AN: 68006

Other (OTH) AF: 0.900 AC: 1893 AN: 2104

Alfa AF: 0.928 Hom.: 39981

Bravo AF: 0.888

Asia WGS AF: 0.904 AC: 3146 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.017
DANN	Benign	0.58
PhyloP100		-2.8

Splicing

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

Other links and lift over

dbSNP: rs10758892; hg19: chr9-7734250;