rs1980946

Positions:

• chr20-49727774-C-G
• chr20-49727774-C-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 0.195 in 152,056 control chromosomes in the GnomAD database, including 4,553 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 0.19 (4553 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.648

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.415 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: 0.195 AC: 29567 AN: 151938 Hom.: 4532 Cov.: 32

Gnomad AFR AF: 0.420

Gnomad AMI AF: 0.0647

Gnomad AMR AF: 0.225

Gnomad ASJ AF: 0.0853

Gnomad EAS AF: 0.206

Gnomad SAS AF: 0.142

Gnomad FIN AF: 0.0877

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.0786

Gnomad OTH AF: 0.179

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

GnomAD4 genome AF: 0.195 AC: 29633 AN: 152056 Hom.: 4553 Cov.: 32 AF XY: 0.194 AC XY: 14401 AN XY: 74332

Gnomad4 AFR AF: 0.420

Gnomad4 AMR AF: 0.225

Gnomad4 ASJ AF: 0.0853

Gnomad4 EAS AF: 0.206

Gnomad4 SAS AF: 0.141

Gnomad4 FIN AF: 0.0877

Gnomad4 NFE AF: 0.0786

Gnomad4 OTH AF: 0.181

Alfa AF: 0.0420 Hom.: 29

Bravo AF: 0.217

Asia WGS AF: 0.165 AC: 573 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.90
DANN	Benign	0.17

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1980946; hg19: chr20-48344311;