rs1980946

Variant names:

• chr20-49727774-C-G
• rs1980946

Your query was ambiguous. Multiple possible variants found:

• chr20-49727774-C-G
• chr20-49727774-C-T

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 0.195 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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.420 AC: 17409 AN: 41438

American (AMR) AF: 0.225 AC: 3434 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.0853 AC: 296 AN: 3472

East Asian (EAS) AF: 0.206 AC: 1063 AN: 5168

South Asian (SAS) AF: 0.141 AC: 681 AN: 4822

European-Finnish (FIN) AF: 0.0877 AC: 928 AN: 10584

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.0786 AC: 5342 AN: 67990

Other (OTH) AF: 0.181 AC: 382 AN: 2114

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
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs1980946; hg19: chr20-48344311;