chr13-26503403-G-A

Variant names:

• chr13-26503403-G-A
• rs17084228
• ENST00000838011.1:n.191G>A

Variant summary

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

The ENST00000838011.1(ENSG00000309044):​n.191G>A 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 0.21 in 152,116 control chromosomes in the GnomAD database, including 3,701 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 0.21 (3701 hom., cov: 33)
• Consequence: ENSG00000309044 ENST00000838011.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.86
• Publications: 5 publications found

Genes affected

ENSG00000309044 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.285 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
ENSG00000309044	ENST00000838011.1	n.191G>A		non_coding_transcript_exon_variant	Exon 1 of 6

Frequencies

GnomAD3 genomes AF: 0.209 AC: 31835 AN: 151998 Hom.: 3696 Cov.: 33

Gnomad AFR AF: 0.286

Gnomad AMI AF: 0.0866

Gnomad AMR AF: 0.292

Gnomad ASJ AF: 0.122

Gnomad EAS AF: 0.159

Gnomad SAS AF: 0.137

Gnomad FIN AF: 0.139

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.210 AC: 31870 AN: 152116 Hom.: 3701 Cov.: 33 AF XY: 0.207 AC XY: 15424 AN XY: 74376

African (AFR) AF: 0.286 AC: 11848 AN: 41460

American (AMR) AF: 0.292 AC: 4459 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.122 AC: 425 AN: 3472

East Asian (EAS) AF: 0.158 AC: 819 AN: 5172

South Asian (SAS) AF: 0.138 AC: 664 AN: 4816

European-Finnish (FIN) AF: 0.139 AC: 1472 AN: 10588

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.171 AC: 11612 AN: 67998

Other (OTH) AF: 0.205 AC: 434 AN: 2116

Alfa AF: 0.185 Hom.: 1612

Bravo AF: 0.228

Asia WGS AF: 0.190 AC: 659 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.2
DANN	Benign	0.62
PhyloP100		-3.9

Splicing

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

Other links and lift over

dbSNP: rs17084228; hg19: chr13-27077540;