5-76769877-T-C

Variant names:

• chr5-76769877-T-C
• rs253088

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 0.642 in 151,298 control chromosomes in the GnomAD database, including 31,915 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 0.64 (31915 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.03
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.77 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: 0.642 AC: 97077 AN: 151182 Hom.: 31884 Cov.: 29

Gnomad AFR AF: 0.777

Gnomad AMI AF: 0.593

Gnomad AMR AF: 0.628

Gnomad ASJ AF: 0.516

Gnomad EAS AF: 0.757

Gnomad SAS AF: 0.476

Gnomad FIN AF: 0.505

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.594

Gnomad OTH AF: 0.650

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

GnomAD4 genome AF: 0.642 AC: 97164 AN: 151298 Hom.: 31915 Cov.: 29 AF XY: 0.635 AC XY: 46882 AN XY: 73884

African (AFR) AF: 0.778 AC: 32088 AN: 41270

American (AMR) AF: 0.628 AC: 9543 AN: 15200

Ashkenazi Jewish (ASJ) AF: 0.516 AC: 1785 AN: 3460

East Asian (EAS) AF: 0.757 AC: 3875 AN: 5122

South Asian (SAS) AF: 0.476 AC: 2275 AN: 4782

European-Finnish (FIN) AF: 0.505 AC: 5245 AN: 10390

Middle Eastern (MID) AF: 0.592 AC: 174 AN: 294

European-Non Finnish (NFE) AF: 0.594 AC: 40286 AN: 67774

Other (OTH) AF: 0.645 AC: 1358 AN: 2104

Alfa AF: 0.608 Hom.: 3587

Bravo AF: 0.660

Asia WGS AF: 0.642 AC: 2226 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.41
DANN	Benign	0.11
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs253088; hg19: chr5-76065702;