13-109744675-T-C

Variant names:

• chr13-109744675-T-C
• rs1556223
• ENST00000836658.1:n.583T>C

Variant summary

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

The ENST00000836658.1(ENSG00000308820):​n.583T>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 0.575 in 152,060 control chromosomes in the GnomAD database, including 25,480 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 (25480 hom., cov: 33)
• Consequence: ENSG00000308820 ENST00000836658.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07
• Publications: 7 publications found

Genes affected

ENSG00000308820 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.672 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000836658.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000308820	ENST00000836658.1		n.583T>C		non_coding_transcript_exon	Exon 1 of 2
	ENSG00000308820	ENST00000836657.1		n.150-580T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.575 AC: 87427 AN: 151940 Hom.: 25469 Cov.: 33

Gnomad AFR AF: 0.485

Gnomad AMI AF: 0.421

Gnomad AMR AF: 0.682

Gnomad ASJ AF: 0.621

Gnomad EAS AF: 0.560

Gnomad SAS AF: 0.540

Gnomad FIN AF: 0.610

Gnomad MID AF: 0.618

Gnomad NFE AF: 0.604

Gnomad OTH AF: 0.587

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

GnomAD4 genome AF: 0.575 AC: 87475 AN: 152060 Hom.: 25480 Cov.: 33 AF XY: 0.577 AC XY: 42876 AN XY: 74308

African (AFR) AF: 0.485 AC: 20089 AN: 41458

American (AMR) AF: 0.683 AC: 10443 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.621 AC: 2156 AN: 3472

East Asian (EAS) AF: 0.560 AC: 2876 AN: 5140

South Asian (SAS) AF: 0.542 AC: 2613 AN: 4824

European-Finnish (FIN) AF: 0.610 AC: 6461 AN: 10590

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.604 AC: 41050 AN: 67964

Other (OTH) AF: 0.581 AC: 1228 AN: 2112

Alfa AF: 0.598 Hom.: 76721

Bravo AF: 0.579

Asia WGS AF: 0.536 AC: 1867 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.028
DANN	Benign	0.31
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs1556223; hg19: chr13-110397022;