rs7039377

chr9-38675468-G-A

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.650

Gnomad4 AMR AF: 0.509

Gnomad4 ASJ AF: 0.603

Gnomad4 EAS AF: 0.458

Gnomad4 SAS AF: 0.477

Gnomad4 FIN AF: 0.551

Gnomad4 NFE AF: 0.492

Gnomad4 OTH AF: 0.536

Alfa AF: 0.502 Hom.: 25697

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

Splicing

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

Publications

LitVar

Other links and lift over

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