13-34032049-A-G

Variant names:

• chr13-34032049-A-G
• rs2321744
• ENST00000747769.1:n.118-211T>C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000747769.1(ENSG00000297413):​n.118-211T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.137 in 152,260 control chromosomes in the GnomAD database, including 1,768 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 0.14 (1768 hom., cov: 33)
• Consequence: ENSG00000297413 ENST00000747769.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.60
• Publications: 7 publications found

Genes affected

ENSG00000297413 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.21).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.21 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000747769.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000297413	ENST00000747769.1		n.118-211T>C		intron	N/A
	ENSG00000297413	ENST00000747770.1		n.-206T>C		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.137 AC: 20808 AN: 152142 Hom.: 1763 Cov.: 33

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.112

Gnomad AMR AF: 0.181

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.100

Gnomad SAS AF: 0.168

Gnomad FIN AF: 0.0820

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.0877

Gnomad OTH AF: 0.145

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

GnomAD4 genome AF: 0.137 AC: 20832 AN: 152260 Hom.: 1768 Cov.: 33 AF XY: 0.137 AC XY: 10216 AN XY: 74466

African (AFR) AF: 0.214 AC: 8878 AN: 41544

American (AMR) AF: 0.181 AC: 2772 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.161 AC: 558 AN: 3470

East Asian (EAS) AF: 0.0999 AC: 518 AN: 5186

South Asian (SAS) AF: 0.168 AC: 810 AN: 4828

European-Finnish (FIN) AF: 0.0820 AC: 870 AN: 10610

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.0877 AC: 5965 AN: 68010

Other (OTH) AF: 0.150 AC: 317 AN: 2114

Alfa AF: 0.109 Hom.: 3159

Bravo AF: 0.151

Asia WGS AF: 0.200 AC: 694 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.21
CADD	Benign	16
DANN	Benign	0.88
PhyloP100		1.6

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2321744;

hg19: chr13-34606186;