rs750160

Positions:

• chr20-720987-T-C

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 0.316 in 152,088 control chromosomes in the GnomAD database, including 9,687 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 0.32 (9687 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.714

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.569 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.315 AC: 47928 AN: 151970 Hom.: 9666 Cov.: 32

Gnomad AFR AF: 0.575

Gnomad AMI AF: 0.179

Gnomad AMR AF: 0.225

Gnomad ASJ AF: 0.225

Gnomad EAS AF: 0.0253

Gnomad SAS AF: 0.130

Gnomad FIN AF: 0.178

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.241

Gnomad OTH AF: 0.316

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

GnomAD4 genome AF: 0.316 AC: 47996 AN: 152088 Hom.: 9687 Cov.: 32 AF XY: 0.306 AC XY: 22728 AN XY: 74348

Gnomad4 AFR AF: 0.575

Gnomad4 AMR AF: 0.225

Gnomad4 ASJ AF: 0.225

Gnomad4 EAS AF: 0.0258

Gnomad4 SAS AF: 0.129

Gnomad4 FIN AF: 0.178

Gnomad4 NFE AF: 0.241

Gnomad4 OTH AF: 0.315

Alfa AF: 0.258 Hom.: 2026

Bravo AF: 0.332

Asia WGS AF: 0.136 AC: 475 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.31
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs750160; hg19: chr20-701631;