rs32720

Positions:

• chr5-165866316-A-G
• chr5-165866316-A-T

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 0.428 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.598

Gnomad4 AMR AF: 0.406

Gnomad4 ASJ AF: 0.437

Gnomad4 EAS AF: 0.443

Gnomad4 SAS AF: 0.360

Gnomad4 FIN AF: 0.460

Gnomad4 NFE AF: 0.331

Gnomad4 OTH AF: 0.393

Alfa AF: 0.348 Hom.: 12305

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs32720; hg19: chr5-165293321;