rs13043313

Variant names:

• chr20-62383213-T-C
• rs13043313
• ENST00000718822.1:n.677T>C

Your query was ambiguous. Multiple possible variants found:

• chr20-62383213-T-C
• chr20-62383213-T-G

Variant summary

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

The ENST00000718822.1(ENSG00000293761):​n.677T>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 0.271 in 152,146 control chromosomes in the GnomAD database, including 5,744 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 0.27 (5744 hom., cov: 32)
• Consequence: ENSG00000293761 ENST00000718822.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.912
• Publications: 13 publications found

Genes affected

ENSG00000293761 (HGNC:):

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 (SAS) allele frequency at 95% confidence interval = 0.381 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
ENSG00000293761	ENST00000718822.1	n.677T>C		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.271 AC: 41135 AN: 152026 Hom.: 5740 Cov.: 32

Gnomad AFR AF: 0.259

Gnomad AMI AF: 0.232

Gnomad AMR AF: 0.286

Gnomad ASJ AF: 0.245

Gnomad EAS AF: 0.148

Gnomad SAS AF: 0.395

Gnomad FIN AF: 0.271

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.277

Gnomad OTH AF: 0.260

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

GnomAD4 genome AF: 0.271 AC: 41157 AN: 152146 Hom.: 5744 Cov.: 32 AF XY: 0.272 AC XY: 20248 AN XY: 74388

African (AFR) AF: 0.259 AC: 10731 AN: 41508

American (AMR) AF: 0.287 AC: 4384 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.245 AC: 850 AN: 3466

East Asian (EAS) AF: 0.148 AC: 766 AN: 5180

South Asian (SAS) AF: 0.396 AC: 1907 AN: 4820

European-Finnish (FIN) AF: 0.271 AC: 2866 AN: 10580

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.277 AC: 18814 AN: 67988

Other (OTH) AF: 0.256 AC: 541 AN: 2110

Alfa AF: 0.268 Hom.: 11238

Bravo AF: 0.267

Asia WGS AF: 0.262 AC: 913 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	0.81
DANN	Benign	0.57
PhyloP100		-0.91

Splicing

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

Other links and lift over

dbSNP: rs13043313; hg19: chr20-60958269;