5-10804410-C-T

Variant names:

• chr5-10804410-C-T
• rs10043680

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 0.76 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
• 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 (NFE) allele frequency at 95% confidence interval = 0.862 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: 0.760 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

African (AFR) AF: 0.661 AC: 27418 AN: 41490

American (AMR) AF: 0.715 AC: 10945 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.813 AC: 2821 AN: 3472

East Asian (EAS) AF: 0.137 AC: 709 AN: 5180

South Asian (SAS) AF: 0.634 AC: 3055 AN: 4822

European-Finnish (FIN) AF: 0.858 AC: 9097 AN: 10606

Middle Eastern (MID) AF: 0.799 AC: 235 AN: 294

European-Non Finnish (NFE) AF: 0.868 AC: 59039 AN: 68018

Other (OTH) AF: 0.752 AC: 1587 AN: 2110

Alfa AF: 0.765 Hom.: 4765

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
PhyloP100		-0.92

Splicing

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

Other links and lift over

dbSNP: rs10043680; hg19: chr5-10804522;