rs235753

Variant names:

• chr20-6788886-G-A
• rs235753

Your query was ambiguous. Multiple possible variants found:

• chr20-6788886-G-A
• chr20-6788886-G-C
• chr20-6788886-G-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 0.412 in 152,080 control chromosomes in the GnomAD database, including 13,580 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 0.41 (13580 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.132
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.543 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: 0.412 AC: 62659 AN: 151964 Hom.: 13556 Cov.: 33

Gnomad AFR AF: 0.549

Gnomad AMI AF: 0.348

Gnomad AMR AF: 0.424

Gnomad ASJ AF: 0.335

Gnomad EAS AF: 0.544

Gnomad SAS AF: 0.364

Gnomad FIN AF: 0.337

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.337

Gnomad OTH AF: 0.413

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

GnomAD4 genome AF: 0.412 AC: 62722 AN: 152080 Hom.: 13580 Cov.: 33 AF XY: 0.414 AC XY: 30793 AN XY: 74348

African (AFR) AF: 0.549 AC: 22751 AN: 41458

American (AMR) AF: 0.424 AC: 6485 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.335 AC: 1162 AN: 3472

East Asian (EAS) AF: 0.543 AC: 2805 AN: 5166

South Asian (SAS) AF: 0.363 AC: 1745 AN: 4810

European-Finnish (FIN) AF: 0.337 AC: 3570 AN: 10580

Middle Eastern (MID) AF: 0.303 AC: 89 AN: 294

European-Non Finnish (NFE) AF: 0.337 AC: 22916 AN: 67982

Other (OTH) AF: 0.418 AC: 882 AN: 2112

Alfa AF: 0.363 Hom.: 32508

Bravo AF: 0.426

Asia WGS AF: 0.437 AC: 1522 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	7.4
DANN	Benign	0.57
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs235753; hg19: chr20-6769533;