13-112435894-G-A

Variant names:

• chr13-112435894-G-A
• rs7992158
• ENST00000732758.1:n.223+39240C>T

Variant summary

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

The ENST00000732758.1(ENSG00000295796):​n.223+39240C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.558 in 152,122 control chromosomes in the GnomAD database, including 24,144 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 0.56 (24144 hom., cov: 33)
• Consequence: ENSG00000295796 ENST00000732758.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27
• Publications: 5 publications found

Genes affected

ENSG00000295796 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.926 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370372	XR_001750036.1	n.384+39240C>T		intron_variant	Intron 1 of 3
LOC105370372	XR_944292.2	n.332+39240C>T		intron_variant	Intron 2 of 4
LOC105370372	XR_944294.2	n.329+39240C>T		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000295796	ENST00000732758.1	n.223+39240C>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.558 AC: 84785 AN: 152004 Hom.: 24138 Cov.: 33

Gnomad AFR AF: 0.525

Gnomad AMI AF: 0.434

Gnomad AMR AF: 0.603

Gnomad ASJ AF: 0.603

Gnomad EAS AF: 0.948

Gnomad SAS AF: 0.609

Gnomad FIN AF: 0.592

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.528

Gnomad OTH AF: 0.565

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

GnomAD4 genome AF: 0.558 AC: 84827 AN: 152122 Hom.: 24144 Cov.: 33 AF XY: 0.562 AC XY: 41822 AN XY: 74362

African (AFR) AF: 0.524 AC: 21735 AN: 41472

American (AMR) AF: 0.604 AC: 9231 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.603 AC: 2092 AN: 3472

East Asian (EAS) AF: 0.948 AC: 4907 AN: 5178

South Asian (SAS) AF: 0.608 AC: 2931 AN: 4818

European-Finnish (FIN) AF: 0.592 AC: 6263 AN: 10588

Middle Eastern (MID) AF: 0.527 AC: 155 AN: 294

European-Non Finnish (NFE) AF: 0.528 AC: 35928 AN: 67990

Other (OTH) AF: 0.565 AC: 1190 AN: 2108

Alfa AF: 0.543 Hom.: 34085

Bravo AF: 0.560

Asia WGS AF: 0.702 AC: 2438 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.31
DANN	Benign	0.44
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs7992158; hg19: chr13-113090208;