rs995480

chr20-51162339-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 0.583 in 152,094 control chromosomes in the GnomAD database, including 27,359 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 0.58 (27359 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00800

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.797 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: 0.582 AC: 88487 AN: 151978 Hom.: 27303 Cov.: 32

Gnomad AFR AF: 0.804

Gnomad AMI AF: 0.532

Gnomad AMR AF: 0.538

Gnomad ASJ AF: 0.512

Gnomad EAS AF: 0.355

Gnomad SAS AF: 0.452

Gnomad FIN AF: 0.447

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.510

Gnomad OTH AF: 0.560

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

GnomAD4 genome AF: 0.583 AC: 88608 AN: 152094 Hom.: 27359 Cov.: 32 AF XY: 0.574 AC XY: 42682 AN XY: 74338

Gnomad4 AFR AF: 0.804

Gnomad4 AMR AF: 0.538

Gnomad4 ASJ AF: 0.512

Gnomad4 EAS AF: 0.355

Gnomad4 SAS AF: 0.454

Gnomad4 FIN AF: 0.447

Gnomad4 NFE AF: 0.510

Gnomad4 OTH AF: 0.563

Alfa AF: 0.531 Hom.: 14155

Bravo AF: 0.597

Asia WGS AF: 0.436 AC: 1520 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	3.4
Dann	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs995480; hg19: chr20-49778876; COSMIC: COSV50954108;