5-85922051-T-C

Variant names:

• chr5-85922051-T-C
• rs1583686

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 0.796 in 152,182 control chromosomes in the GnomAD database, including 48,492 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 0.80 (48492 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.810
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.856 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: 0.796 AC: 121081 AN: 152064 Hom.: 48463 Cov.: 32

Gnomad AFR AF: 0.725

Gnomad AMI AF: 0.793

Gnomad AMR AF: 0.868

Gnomad ASJ AF: 0.708

Gnomad EAS AF: 0.823

Gnomad SAS AF: 0.822

Gnomad FIN AF: 0.839

Gnomad MID AF: 0.775

Gnomad NFE AF: 0.817

Gnomad OTH AF: 0.816

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

GnomAD4 genome AF: 0.796 AC: 121162 AN: 152182 Hom.: 48492 Cov.: 32 AF XY: 0.798 AC XY: 59391 AN XY: 74390

African (AFR) AF: 0.725 AC: 30084 AN: 41502

American (AMR) AF: 0.868 AC: 13276 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.708 AC: 2459 AN: 3472

East Asian (EAS) AF: 0.824 AC: 4254 AN: 5162

South Asian (SAS) AF: 0.821 AC: 3953 AN: 4816

European-Finnish (FIN) AF: 0.839 AC: 8893 AN: 10600

Middle Eastern (MID) AF: 0.759 AC: 223 AN: 294

European-Non Finnish (NFE) AF: 0.817 AC: 55577 AN: 68026

Other (OTH) AF: 0.816 AC: 1721 AN: 2110

Alfa AF: 0.807 Hom.: 74801

Bravo AF: 0.798

Asia WGS AF: 0.797 AC: 2772 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.5
DANN	Benign	0.66
PhyloP100		-0.81

Splicing

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

Other links and lift over

dbSNP: rs1583686; hg19: chr5-85217869;