5-80624254-C-T

Variant names:

• chr5-80624254-C-T
• rs12517451

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B.

Score: -12 - Benign

-12

BP4_StrongBA1

The variant allele was found at a frequency of 0.207 in 151,894 control chromosomes in the GnomAD database, including 3,642 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 0.21 (3642 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.36
• Publications: 24 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.32 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: 0.207 AC: 31417 AN: 151776 Hom.: 3637 Cov.: 31

Gnomad AFR AF: 0.0871

Gnomad AMI AF: 0.139

Gnomad AMR AF: 0.237

Gnomad ASJ AF: 0.250

Gnomad EAS AF: 0.333

Gnomad SAS AF: 0.304

Gnomad FIN AF: 0.277

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.245

Gnomad OTH AF: 0.213

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

GnomAD4 genome AF: 0.207 AC: 31441 AN: 151894 Hom.: 3642 Cov.: 31 AF XY: 0.212 AC XY: 15707 AN XY: 74208

African (AFR) AF: 0.0871 AC: 3610 AN: 41460

American (AMR) AF: 0.237 AC: 3614 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.250 AC: 866 AN: 3466

East Asian (EAS) AF: 0.333 AC: 1705 AN: 5122

South Asian (SAS) AF: 0.304 AC: 1463 AN: 4806

European-Finnish (FIN) AF: 0.277 AC: 2918 AN: 10530

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.245 AC: 16628 AN: 67946

Other (OTH) AF: 0.215 AC: 454 AN: 2112

Alfa AF: 0.223 Hom.: 9153

Bravo AF: 0.195

Asia WGS AF: 0.320 AC: 1114 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.4
DANN	Benign	0.53
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs12517451; hg19: chr5-79920073;