ENST00000732758.1:n.223+39240C>T

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000732758.1. 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
	ENSG00000295796	ENST00000732758.1		n.223+39240C>T		intron	N/A

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 v4.9

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;