rs1573998

Variant names:

• chr5-56980666-T-C
• rs1573998

Your query was ambiguous. Multiple possible variants found:

• chr5-56980666-T-C
• chr5-56980666-T-G

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 0.756 in 152,140 control chromosomes in the GnomAD database, including 43,737 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 0.76 (43737 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0140
• Publications: 14 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.791 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: 0.755 AC: 114841 AN: 152022 Hom.: 43682 Cov.: 32

Gnomad AFR AF: 0.730

Gnomad AMI AF: 0.702

Gnomad AMR AF: 0.701

Gnomad ASJ AF: 0.793

Gnomad EAS AF: 0.555

Gnomad SAS AF: 0.701

Gnomad FIN AF: 0.785

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.797

Gnomad OTH AF: 0.761

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

GnomAD4 genome AF: 0.756 AC: 114953 AN: 152140 Hom.: 43737 Cov.: 32 AF XY: 0.750 AC XY: 55808 AN XY: 74380

African (AFR) AF: 0.730 AC: 30276 AN: 41482

American (AMR) AF: 0.701 AC: 10709 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.793 AC: 2754 AN: 3472

East Asian (EAS) AF: 0.555 AC: 2877 AN: 5184

South Asian (SAS) AF: 0.702 AC: 3387 AN: 4828

European-Finnish (FIN) AF: 0.785 AC: 8307 AN: 10576

Middle Eastern (MID) AF: 0.762 AC: 224 AN: 294

European-Non Finnish (NFE) AF: 0.797 AC: 54169 AN: 67998

Other (OTH) AF: 0.764 AC: 1611 AN: 2110

Alfa AF: 0.769 Hom.: 59611

Bravo AF: 0.746

Asia WGS AF: 0.639 AC: 2223 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.4
DANN	Benign	0.56
PhyloP100		0.014

Splicing

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

Other links and lift over

dbSNP: rs1573998; hg19: chr5-56276493;