rs11697848

Positions:

• chr20-49958778-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 0.0369 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.0370 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

Gnomad4 AFR AF: 0.0143

Gnomad4 AMR AF: 0.0506

Gnomad4 ASJ AF: 0.0329

Gnomad4 EAS AF: 0.0925

Gnomad4 SAS AF: 0.0183

Gnomad4 FIN AF: 0.0150

Gnomad4 NFE AF: 0.0481

Gnomad4 OTH AF: 0.0503

Alfa AF: 0.0426 Hom.: 61

Bravo AF: 0.0396

Asia WGS AF: 0.0510 AC: 179 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11697848; hg19: chr20-48575315;