5-10804410-C-T

Position:

• chr5-10804410-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.76 in 152,202 control chromosomes in the GnomAD database, including 45,795 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 (45795 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.921

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.862 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.760 AC: 115568 AN: 152084 Hom.: 45780 Cov.: 33

Gnomad AFR AF: 0.661

Gnomad AMI AF: 0.785

Gnomad AMR AF: 0.716

Gnomad ASJ AF: 0.813

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.633

Gnomad FIN AF: 0.858

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.868

Gnomad OTH AF: 0.760

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

GnomAD4 genome AF: 0.760 AC: 115622 AN: 152202 Hom.: 45795 Cov.: 33 AF XY: 0.753 AC XY: 56051 AN XY: 74410

Gnomad4 AFR AF: 0.661

Gnomad4 AMR AF: 0.715

Gnomad4 ASJ AF: 0.813

Gnomad4 EAS AF: 0.137

Gnomad4 SAS AF: 0.634

Gnomad4 FIN AF: 0.858

Gnomad4 NFE AF: 0.868

Gnomad4 OTH AF: 0.752

Alfa AF: 0.770 Hom.: 4588

Bravo AF: 0.742

Asia WGS AF: 0.413 AC: 1442 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	0.11
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10043680; hg19: chr5-10804522;