rs7040848

Variant names:

• chr9-85238445-G-A
• rs7040848

Your query was ambiguous. Multiple possible variants found:

• chr9-85238445-G-A
• chr9-85238445-G-C
• chr9-85238445-G-T

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 0.695 in 151,994 control chromosomes in the GnomAD database, including 38,645 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 0.70 (38645 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.724
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.908 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: 0.695 AC: 105571 AN: 151876 Hom.: 38578 Cov.: 32

Gnomad AFR AF: 0.916

Gnomad AMI AF: 0.349

Gnomad AMR AF: 0.683

Gnomad ASJ AF: 0.621

Gnomad EAS AF: 0.882

Gnomad SAS AF: 0.707

Gnomad FIN AF: 0.643

Gnomad MID AF: 0.694

Gnomad NFE AF: 0.565

Gnomad OTH AF: 0.699

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

GnomAD4 genome AF: 0.695 AC: 105697 AN: 151994 Hom.: 38645 Cov.: 32 AF XY: 0.699 AC XY: 51954 AN XY: 74288

African (AFR) AF: 0.916 AC: 38009 AN: 41492

American (AMR) AF: 0.683 AC: 10414 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.621 AC: 2153 AN: 3466

East Asian (EAS) AF: 0.882 AC: 4573 AN: 5184

South Asian (SAS) AF: 0.707 AC: 3402 AN: 4812

European-Finnish (FIN) AF: 0.643 AC: 6785 AN: 10544

Middle Eastern (MID) AF: 0.712 AC: 208 AN: 292

European-Non Finnish (NFE) AF: 0.565 AC: 38352 AN: 67928

Other (OTH) AF: 0.703 AC: 1484 AN: 2110

Alfa AF: 0.608 Hom.: 18259

Bravo AF: 0.711

Asia WGS AF: 0.799 AC: 2770 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	4.6
DANN	Benign	0.68
PhyloP100		0.72

Splicing

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

Other links and lift over

dbSNP: rs7040848; hg19: chr9-87853360;