rs1037597

Variant names:

• chr5-98447342-T-C
• rs1037597

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 0.564 in 152,106 control chromosomes in the GnomAD database, including 24,630 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 0.56 (24630 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.291
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.671 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.564 AC: 85710 AN: 151988 Hom.: 24615 Cov.: 33

Gnomad AFR AF: 0.678

Gnomad AMI AF: 0.627

Gnomad AMR AF: 0.492

Gnomad ASJ AF: 0.500

Gnomad EAS AF: 0.435

Gnomad SAS AF: 0.598

Gnomad FIN AF: 0.449

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.539

Gnomad OTH AF: 0.534

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

GnomAD4 genome AF: 0.564 AC: 85768 AN: 152106 Hom.: 24630 Cov.: 33 AF XY: 0.558 AC XY: 41484 AN XY: 74354

African (AFR) AF: 0.678 AC: 28120 AN: 41486

American (AMR) AF: 0.492 AC: 7520 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 1737 AN: 3472

East Asian (EAS) AF: 0.435 AC: 2255 AN: 5186

South Asian (SAS) AF: 0.594 AC: 2865 AN: 4822

European-Finnish (FIN) AF: 0.449 AC: 4751 AN: 10576

Middle Eastern (MID) AF: 0.527 AC: 155 AN: 294

European-Non Finnish (NFE) AF: 0.540 AC: 36665 AN: 67956

Other (OTH) AF: 0.534 AC: 1128 AN: 2114

Alfa AF: 0.553 Hom.: 11934

Bravo AF: 0.572

Asia WGS AF: 0.558 AC: 1941 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.8
DANN	Benign	0.80
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs1037597; hg19: chr5-97783046;