rs235746

Variant names:

• chr20-6800984-C-T
• rs235746

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 0.183 in 152,154 control chromosomes in the GnomAD database, including 3,741 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 0.18 (3741 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.652

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.367 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: 0.183 AC: 27801 AN: 152036 Hom.: 3734 Cov.: 33

Gnomad AFR AF: 0.372

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.202

Gnomad ASJ AF: 0.0389

Gnomad EAS AF: 0.240

Gnomad SAS AF: 0.0950

Gnomad FIN AF: 0.0867

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0912

Gnomad OTH AF: 0.159

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

GnomAD4 genome AF: 0.183 AC: 27843 AN: 152154 Hom.: 3741 Cov.: 33 AF XY: 0.181 AC XY: 13501 AN XY: 74408

Gnomad4 AFR AF: 0.372

Gnomad4 AMR AF: 0.202

Gnomad4 ASJ AF: 0.0389

Gnomad4 EAS AF: 0.239

Gnomad4 SAS AF: 0.0955

Gnomad4 FIN AF: 0.0867

Gnomad4 NFE AF: 0.0911

Gnomad4 OTH AF: 0.165

Alfa AF: 0.147 Hom.: 551

Bravo AF: 0.199

Asia WGS AF: 0.197 AC: 687 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.4
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs235746; hg19: chr20-6781631;