chr5-85310710-T-C

Variant names:

• chr5-85310710-T-C
• rs4920799

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 0.806 in 152,130 control chromosomes in the GnomAD database, including 49,682 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 0.81 (49682 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.210

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.844 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: 0.807 AC: 122603 AN: 152012 Hom.: 49666 Cov.: 31

Gnomad AFR AF: 0.756

Gnomad AMI AF: 0.913

Gnomad AMR AF: 0.764

Gnomad ASJ AF: 0.867

Gnomad EAS AF: 0.630

Gnomad SAS AF: 0.819

Gnomad FIN AF: 0.837

Gnomad MID AF: 0.848

Gnomad NFE AF: 0.850

Gnomad OTH AF: 0.798

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

GnomAD4 genome AF: 0.806 AC: 122675 AN: 152130 Hom.: 49682 Cov.: 31 AF XY: 0.803 AC XY: 59686 AN XY: 74350

Gnomad4 AFR AF: 0.755

Gnomad4 AMR AF: 0.764

Gnomad4 ASJ AF: 0.867

Gnomad4 EAS AF: 0.630

Gnomad4 SAS AF: 0.819

Gnomad4 FIN AF: 0.837

Gnomad4 NFE AF: 0.850

Gnomad4 OTH AF: 0.799

Alfa AF: 0.841 Hom.: 77517

Bravo AF: 0.801

Asia WGS AF: 0.736 AC: 2562 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.3
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4920799; hg19: chr5-84606528;