13-109605379-T-C

Variant names:

• chr13-109605379-T-C
• rs6492208
• ENST00000837748.1:n.1222A>G

Variant summary

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

The ENST00000837748.1(ENSG00000309005):​n.1222A>G 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 0.448 in 152,064 control chromosomes in the GnomAD database, including 15,817 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 0.45 (15817 hom., cov: 33)
• Consequence: ENSG00000309005 ENST00000837748.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.18
• Publications: 7 publications found

Genes affected

ENSG00000309005 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.563 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124903210	XR_007063870.1	n.940+830A>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000309005	ENST00000837748.1	n.1222A>G		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000285534	ENST00000650264.1	n.759-34221A>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.448 AC: 68117 AN: 151946 Hom.: 15794 Cov.: 33

Gnomad AFR AF: 0.548

Gnomad AMI AF: 0.307

Gnomad AMR AF: 0.465

Gnomad ASJ AF: 0.374

Gnomad EAS AF: 0.555

Gnomad SAS AF: 0.580

Gnomad FIN AF: 0.359

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.386

Gnomad OTH AF: 0.436

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

GnomAD4 genome AF: 0.448 AC: 68186 AN: 152064 Hom.: 15817 Cov.: 33 AF XY: 0.452 AC XY: 33609 AN XY: 74334

African (AFR) AF: 0.548 AC: 22727 AN: 41466

American (AMR) AF: 0.465 AC: 7099 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.374 AC: 1300 AN: 3472

East Asian (EAS) AF: 0.555 AC: 2866 AN: 5164

South Asian (SAS) AF: 0.581 AC: 2801 AN: 4822

European-Finnish (FIN) AF: 0.359 AC: 3796 AN: 10570

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.386 AC: 26269 AN: 67974

Other (OTH) AF: 0.436 AC: 922 AN: 2116

Alfa AF: 0.412 Hom.: 25618

Bravo AF: 0.456

Asia WGS AF: 0.532 AC: 1850 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.0
DANN	Benign	0.50
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs6492208; hg19: chr13-110257726;