rs235710

Variant names:

• chr20-6759719-C-T
• rs235710

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 0.458 in 152,028 control chromosomes in the GnomAD database, including 16,161 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 0.46 (16161 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.515 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: 0.458 AC: 69587 AN: 151910 Hom.: 16166 Cov.: 31

Gnomad AFR AF: 0.448

Gnomad AMI AF: 0.424

Gnomad AMR AF: 0.386

Gnomad ASJ AF: 0.503

Gnomad EAS AF: 0.532

Gnomad SAS AF: 0.457

Gnomad FIN AF: 0.521

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.462

Gnomad OTH AF: 0.477

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

GnomAD4 genome AF: 0.458 AC: 69614 AN: 152028 Hom.: 16161 Cov.: 31 AF XY: 0.457 AC XY: 33980 AN XY: 74306

African (AFR) AF: 0.448 AC: 18584 AN: 41470

American (AMR) AF: 0.386 AC: 5887 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.503 AC: 1746 AN: 3470

East Asian (EAS) AF: 0.531 AC: 2739 AN: 5154

South Asian (SAS) AF: 0.455 AC: 2188 AN: 4814

European-Finnish (FIN) AF: 0.521 AC: 5510 AN: 10578

Middle Eastern (MID) AF: 0.548 AC: 161 AN: 294

European-Non Finnish (NFE) AF: 0.462 AC: 31404 AN: 67958

Other (OTH) AF: 0.478 AC: 1008 AN: 2108

Alfa AF: 0.458 Hom.: 53609

Bravo AF: 0.447

Asia WGS AF: 0.473 AC: 1647 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.16
DANN	Benign	0.50
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs235710; hg19: chr20-6740366;