rs7039377

Variant names:

• chr9-38675468-G-A
• rs7039377

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 0.543 in 151,962 control chromosomes in the GnomAD database, including 22,733 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 0.54 (22733 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.197
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.643 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: 0.543 AC: 82390 AN: 151844 Hom.: 22699 Cov.: 32

Gnomad AFR AF: 0.650

Gnomad AMI AF: 0.574

Gnomad AMR AF: 0.509

Gnomad ASJ AF: 0.603

Gnomad EAS AF: 0.458

Gnomad SAS AF: 0.477

Gnomad FIN AF: 0.551

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.492

Gnomad OTH AF: 0.536

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

GnomAD4 genome AF: 0.543 AC: 82477 AN: 151962 Hom.: 22733 Cov.: 32 AF XY: 0.544 AC XY: 40423 AN XY: 74284

African (AFR) AF: 0.650 AC: 26935 AN: 41446

American (AMR) AF: 0.509 AC: 7769 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.603 AC: 2092 AN: 3470

East Asian (EAS) AF: 0.458 AC: 2366 AN: 5164

South Asian (SAS) AF: 0.477 AC: 2303 AN: 4824

European-Finnish (FIN) AF: 0.551 AC: 5805 AN: 10536

Middle Eastern (MID) AF: 0.531 AC: 156 AN: 294

European-Non Finnish (NFE) AF: 0.492 AC: 33400 AN: 67946

Other (OTH) AF: 0.536 AC: 1129 AN: 2108

Alfa AF: 0.517 Hom.: 39686

Bravo AF: 0.544

Asia WGS AF: 0.474 AC: 1651 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.93
DANN	Benign	0.41
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs7039377; hg19: chr9-38675465; COSMIC: COSV72760998;