chr13-42728389-C-T

Variant names:

• chr13-42728389-C-T
• rs1323603
• ENST00000799325.1:n.356-7688G>A

Variant summary

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

The ENST00000799325.1(ENSG00000304062):​n.356-7688G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.961 in 152,252 control chromosomes in the GnomAD database, including 70,530 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 0.96 (70530 hom., cov: 33)
• Consequence: ENSG00000304062 ENST00000799325.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.402
• Publications: 0 publications found

Genes affected

ENSG00000304062 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.992 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124903164	XM_047430822.1	c.131-7688G>A		intron_variant	Intron 1 of 2		XP_047286778.1
LOC124903164	XR_007063769.1	n.671-7688G>A		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000304062	ENST00000799325.1	n.356-7688G>A		intron_variant	Intron 1 of 3
ENSG00000304062	ENST00000799326.1	n.762-7688G>A		intron_variant	Intron 2 of 3
ENSG00000304062	ENST00000799327.1	n.359-7688G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.961 AC: 146235 AN: 152134 Hom.: 70492 Cov.: 33

Gnomad AFR AF: 0.870

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.985

Gnomad ASJ AF: 0.976

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.999

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.953

Gnomad NFE AF: 0.998

Gnomad OTH AF: 0.970

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

GnomAD4 genome AF: 0.961 AC: 146331 AN: 152252 Hom.: 70530 Cov.: 33 AF XY: 0.962 AC XY: 71637 AN XY: 74448

African (AFR) AF: 0.870 AC: 36147 AN: 41538

American (AMR) AF: 0.985 AC: 15036 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.976 AC: 3389 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5190 AN: 5190

South Asian (SAS) AF: 0.999 AC: 4822 AN: 4826

European-Finnish (FIN) AF: 1.00 AC: 10623 AN: 10626

Middle Eastern (MID) AF: 0.952 AC: 280 AN: 294

European-Non Finnish (NFE) AF: 0.998 AC: 67880 AN: 68010

Other (OTH) AF: 0.971 AC: 2052 AN: 2114

Alfa AF: 0.985 Hom.: 44080

Bravo AF: 0.956

Asia WGS AF: 0.988 AC: 3438 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.43
DANN	Benign	0.26
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs1323603; hg19: chr13-43302525;