rs1169791

Variant names:

• chr13-42696381-C-T
• rs1169791
• ENST00000799325.1:n.507-16774G>A

Variant summary

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

The ENST00000799325.1(ENSG00000304062):​n.507-16774G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.485 in 151,980 control chromosomes in the GnomAD database, including 19,181 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 0.48 (19181 hom., cov: 32)
• Consequence: ENSG00000304062 ENST00000799325.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.379
• Publications: 5 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.607 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000304062	ENST00000799325.1	n.507-16774G>A		intron_variant	Intron 2 of 3
ENSG00000304076	ENST00000799486.1	n.161+1999C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.485 AC: 73664 AN: 151862 Hom.: 19171 Cov.: 32

Gnomad AFR AF: 0.294

Gnomad AMI AF: 0.641

Gnomad AMR AF: 0.410

Gnomad ASJ AF: 0.559

Gnomad EAS AF: 0.625

Gnomad SAS AF: 0.624

Gnomad FIN AF: 0.490

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.590

Gnomad OTH AF: 0.499

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

GnomAD4 genome AF: 0.485 AC: 73690 AN: 151980 Hom.: 19181 Cov.: 32 AF XY: 0.483 AC XY: 35847 AN XY: 74290

African (AFR) AF: 0.294 AC: 12165 AN: 41438

American (AMR) AF: 0.410 AC: 6262 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.559 AC: 1941 AN: 3470

East Asian (EAS) AF: 0.625 AC: 3222 AN: 5154

South Asian (SAS) AF: 0.624 AC: 3006 AN: 4818

European-Finnish (FIN) AF: 0.490 AC: 5170 AN: 10542

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

European-Non Finnish (NFE) AF: 0.590 AC: 40119 AN: 67956

Other (OTH) AF: 0.505 AC: 1065 AN: 2108

Alfa AF: 0.562 Hom.: 103120

Bravo AF: 0.467

Asia WGS AF: 0.591 AC: 2055 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.4
DANN	Benign	0.52
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs1169791; hg19: chr13-43270517;