rs7038852

Variant names:

• chr9-21165323-G-A
• rs7038852

Your query was ambiguous. Multiple possible variants found:

• chr9-21165323-G-A
• chr9-21165323-G-C

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 0.598 in 151,964 control chromosomes in the GnomAD database, including 27,531 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 0.60 (27531 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.56
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.854 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: 0.598 AC: 90784 AN: 151846 Hom.: 27505 Cov.: 32

Gnomad AFR AF: 0.531

Gnomad AMI AF: 0.649

Gnomad AMR AF: 0.636

Gnomad ASJ AF: 0.611

Gnomad EAS AF: 0.874

Gnomad SAS AF: 0.713

Gnomad FIN AF: 0.590

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.600

Gnomad OTH AF: 0.608

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

GnomAD4 genome AF: 0.598 AC: 90857 AN: 151964 Hom.: 27531 Cov.: 32 AF XY: 0.602 AC XY: 44739 AN XY: 74264

African (AFR) AF: 0.530 AC: 21989 AN: 41458

American (AMR) AF: 0.636 AC: 9707 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.611 AC: 2118 AN: 3464

East Asian (EAS) AF: 0.875 AC: 4542 AN: 5192

South Asian (SAS) AF: 0.713 AC: 3431 AN: 4812

European-Finnish (FIN) AF: 0.590 AC: 6201 AN: 10518

Middle Eastern (MID) AF: 0.626 AC: 184 AN: 294

European-Non Finnish (NFE) AF: 0.601 AC: 40800 AN: 67938

Other (OTH) AF: 0.613 AC: 1294 AN: 2112

Alfa AF: 0.590 Hom.: 3877

Bravo AF: 0.600

Asia WGS AF: 0.777 AC: 2697 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.042
DANN	Benign	0.15
PhyloP100		-2.6

Splicing

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

Other links and lift over

dbSNP: rs7038852; hg19: chr9-21165322; COSMIC: COSV63062771;