rs2597279

Variant names:

• chr7-37626246-G-A
• rs2597279

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 0.696 in 151,420 control chromosomes in the GnomAD database, including 36,843 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 (36843 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.108

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.723 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: 0.696 AC: 105365 AN: 151302 Hom.: 36818 Cov.: 32

Gnomad AFR AF: 0.730

Gnomad AMI AF: 0.659

Gnomad AMR AF: 0.709

Gnomad ASJ AF: 0.693

Gnomad EAS AF: 0.717

Gnomad SAS AF: 0.733

Gnomad FIN AF: 0.719

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.665

Gnomad OTH AF: 0.712

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

GnomAD4 genome AF: 0.696 AC: 105436 AN: 151420 Hom.: 36843 Cov.: 32 AF XY: 0.700 AC XY: 51827 AN XY: 74014

Gnomad4 AFR AF: 0.730

Gnomad4 AMR AF: 0.710

Gnomad4 ASJ AF: 0.693

Gnomad4 EAS AF: 0.716

Gnomad4 SAS AF: 0.733

Gnomad4 FIN AF: 0.719

Gnomad4 NFE AF: 0.665

Gnomad4 OTH AF: 0.708

Alfa AF: 0.650 Hom.: 7052

Bravo AF: 0.702

Asia WGS AF: 0.707 AC: 2440 AN: 3456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	3.4
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2597279; hg19: chr7-37665849;