5-121801286-A-G

Variant names:

• chr5-121801286-A-G
• rs10041728

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.703 in 152,062 control chromosomes in the GnomAD database, including 45,317 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 0.70 (45317 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.623
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.45).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.92 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: 0.703 AC: 106855 AN: 151944 Hom.: 45319 Cov.: 32

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.950

Gnomad AMR AF: 0.831

Gnomad ASJ AF: 0.888

Gnomad EAS AF: 0.782

Gnomad SAS AF: 0.835

Gnomad FIN AF: 0.890

Gnomad MID AF: 0.801

Gnomad NFE AF: 0.926

Gnomad OTH AF: 0.743

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

GnomAD4 genome AF: 0.703 AC: 106850 AN: 152062 Hom.: 45317 Cov.: 32 AF XY: 0.707 AC XY: 52542 AN XY: 74322

African (AFR) AF: 0.193 AC: 8008 AN: 41492

American (AMR) AF: 0.830 AC: 12659 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.888 AC: 3080 AN: 3468

East Asian (EAS) AF: 0.782 AC: 4020 AN: 5142

South Asian (SAS) AF: 0.835 AC: 4026 AN: 4824

European-Finnish (FIN) AF: 0.890 AC: 9433 AN: 10598

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

European-Non Finnish (NFE) AF: 0.926 AC: 62947 AN: 67974

Other (OTH) AF: 0.746 AC: 1576 AN: 2112

Alfa AF: 0.797 Hom.: 23075

Bravo AF: 0.674

Asia WGS AF: 0.766 AC: 2663 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.45
CADD	Benign	8.6
DANN	Benign	0.70
PhyloP100		0.62

Splicing

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

Other links and lift over

dbSNP: rs10041728; hg19: chr5-121136981;