rs235746

Variant names:

• chr20-6800984-C-T
• rs235746

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 0.183 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.372 AC: 15437 AN: 41494

American (AMR) AF: 0.202 AC: 3085 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0389 AC: 135 AN: 3472

East Asian (EAS) AF: 0.239 AC: 1236 AN: 5166

South Asian (SAS) AF: 0.0955 AC: 461 AN: 4826

European-Finnish (FIN) AF: 0.0867 AC: 919 AN: 10596

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0911 AC: 6198 AN: 68012

Other (OTH) AF: 0.165 AC: 348 AN: 2108

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
PhyloP100		0.65

Splicing

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

Other links and lift over

dbSNP: rs235746; hg19: chr20-6781631;