chr20-49958778-C-T

Variant names:

• chr20-49958778-C-T
• rs11697848

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 0.0369 in 151,982 control chromosomes in the GnomAD database, including 146 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 0.037 (146 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07
• Publications: 17 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0857 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.0370 AC: 5613 AN: 151864 Hom.: 146 Cov.: 31

Gnomad AFR AF: 0.0144

Gnomad AMI AF: 0.0285

Gnomad AMR AF: 0.0506

Gnomad ASJ AF: 0.0329

Gnomad EAS AF: 0.0927

Gnomad SAS AF: 0.0181

Gnomad FIN AF: 0.0150

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0481

Gnomad OTH AF: 0.0499

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

GnomAD4 genome AF: 0.0369 AC: 5614 AN: 151982 Hom.: 146 Cov.: 31 AF XY: 0.0360 AC XY: 2677 AN XY: 74290

African (AFR) AF: 0.0143 AC: 594 AN: 41460

American (AMR) AF: 0.0506 AC: 770 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.0329 AC: 114 AN: 3470

East Asian (EAS) AF: 0.0925 AC: 477 AN: 5154

South Asian (SAS) AF: 0.0183 AC: 88 AN: 4806

European-Finnish (FIN) AF: 0.0150 AC: 159 AN: 10582

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0481 AC: 3272 AN: 67974

Other (OTH) AF: 0.0503 AC: 106 AN: 2106

Alfa AF: 0.0444 Hom.: 304

Bravo AF: 0.0396

Asia WGS AF: 0.0510 AC: 179 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.7
DANN	Benign	0.69
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs11697848; hg19: chr20-48575315;