5-80571390-G-T

Variant names:

• chr5-80571390-G-T
• rs249209

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 0.542 in 151,950 control chromosomes in the GnomAD database, including 24,218 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 (24218 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.418
• Publications: 15 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.934 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: 0.542 AC: 82317 AN: 151832 Hom.: 24204 Cov.: 32

Gnomad AFR AF: 0.315

Gnomad AMI AF: 0.633

Gnomad AMR AF: 0.658

Gnomad ASJ AF: 0.632

Gnomad EAS AF: 0.957

Gnomad SAS AF: 0.568

Gnomad FIN AF: 0.697

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.591

Gnomad OTH AF: 0.542

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

GnomAD4 genome AF: 0.542 AC: 82347 AN: 151950 Hom.: 24218 Cov.: 32 AF XY: 0.550 AC XY: 40811 AN XY: 74260

African (AFR) AF: 0.314 AC: 13013 AN: 41378

American (AMR) AF: 0.659 AC: 10071 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.632 AC: 2193 AN: 3468

East Asian (EAS) AF: 0.957 AC: 4954 AN: 5178

South Asian (SAS) AF: 0.568 AC: 2728 AN: 4804

European-Finnish (FIN) AF: 0.697 AC: 7361 AN: 10556

Middle Eastern (MID) AF: 0.507 AC: 149 AN: 294

European-Non Finnish (NFE) AF: 0.591 AC: 40146 AN: 67964

Other (OTH) AF: 0.546 AC: 1155 AN: 2114

Alfa AF: 0.580 Hom.: 107187

Bravo AF: 0.533

Asia WGS AF: 0.718 AC: 2494 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.36
DANN	Benign	0.77
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs249209; hg19: chr5-79867209;