20-57415349-T-C

Variant names:

• chr20-57415349-T-C
• rs737092
• ENST00000827829.1:n.827T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000827829.1(ENSG00000307683):​n.827T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.576 in 152,094 control chromosomes in the GnomAD database, including 26,385 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 0.58 (26385 hom., cov: 33)
• Consequence: ENSG00000307683 ENST00000827829.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.346
• Publications: 28 publications found

Genes affected

ENSG00000307683 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.735 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
ENSG00000307683	ENST00000827829.1	n.827T>C		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.576 AC: 87559 AN: 151974 Hom.: 26329 Cov.: 33

Gnomad AFR AF: 0.742

Gnomad AMI AF: 0.653

Gnomad AMR AF: 0.650

Gnomad ASJ AF: 0.486

Gnomad EAS AF: 0.455

Gnomad SAS AF: 0.402

Gnomad FIN AF: 0.519

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.493

Gnomad OTH AF: 0.581

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

GnomAD4 genome AF: 0.576 AC: 87680 AN: 152094 Hom.: 26385 Cov.: 33 AF XY: 0.575 AC XY: 42750 AN XY: 74366

African (AFR) AF: 0.742 AC: 30783 AN: 41486

American (AMR) AF: 0.650 AC: 9943 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.486 AC: 1687 AN: 3472

East Asian (EAS) AF: 0.456 AC: 2350 AN: 5158

South Asian (SAS) AF: 0.402 AC: 1942 AN: 4826

European-Finnish (FIN) AF: 0.519 AC: 5489 AN: 10572

Middle Eastern (MID) AF: 0.534 AC: 157 AN: 294

European-Non Finnish (NFE) AF: 0.493 AC: 33504 AN: 67970

Other (OTH) AF: 0.584 AC: 1231 AN: 2108

Alfa AF: 0.540 Hom.: 9455

Bravo AF: 0.598

Asia WGS AF: 0.502 AC: 1747 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	8.5
DANN	Benign	0.62
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs737092; hg19: chr20-55990405; COSMIC: COSV60105446;