5-165866316-A-G

Variant names:

• chr5-165866316-A-G
• rs32720

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 0.428 in 151,974 control chromosomes in the GnomAD database, including 14,901 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 0.43 (14901 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.466
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.591 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: 0.428 AC: 64946 AN: 151856 Hom.: 14882 Cov.: 32

Gnomad AFR AF: 0.598

Gnomad AMI AF: 0.246

Gnomad AMR AF: 0.405

Gnomad ASJ AF: 0.437

Gnomad EAS AF: 0.443

Gnomad SAS AF: 0.360

Gnomad FIN AF: 0.460

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.331

Gnomad OTH AF: 0.396

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

GnomAD4 genome AF: 0.428 AC: 64998 AN: 151974 Hom.: 14901 Cov.: 32 AF XY: 0.433 AC XY: 32130 AN XY: 74288

African (AFR) AF: 0.598 AC: 24751 AN: 41418

American (AMR) AF: 0.406 AC: 6199 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.437 AC: 1516 AN: 3470

East Asian (EAS) AF: 0.443 AC: 2291 AN: 5174

South Asian (SAS) AF: 0.360 AC: 1738 AN: 4826

European-Finnish (FIN) AF: 0.460 AC: 4858 AN: 10558

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.331 AC: 22482 AN: 67932

Other (OTH) AF: 0.393 AC: 832 AN: 2116

Alfa AF: 0.363 Hom.: 32396

Bravo AF: 0.435

Asia WGS AF: 0.413 AC: 1432 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	0.20
DANN	Benign	0.82
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs32720; hg19: chr5-165293321;