13-21811591-T-C

Variant names:

• chr13-21811591-T-C
• rs9316567
• ENST00000785194.1:n.221-1967T>C

Variant summary

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

The ENST00000785194.1(ENSG00000302249):​n.221-1967T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.589 in 145,790 control chromosomes in the GnomAD database, including 25,681 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 0.59 (25681 hom., cov: 22)
• Consequence: ENSG00000302249 ENST00000785194.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.333
• Publications: 2 publications found

Genes affected

ENSG00000302249 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.654 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124903132	XR_007063714.1	n.216-1967T>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000302249	ENST00000785194.1	n.221-1967T>C		intron_variant	Intron 1 of 2
ENSG00000302249	ENST00000785195.1	n.236-1967T>C		intron_variant	Intron 1 of 2
ENSG00000302249	ENST00000785196.1	n.239-1967T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.589 AC: 85773 AN: 145676 Hom.: 25665 Cov.: 22

Gnomad AFR AF: 0.507

Gnomad AMI AF: 0.717

Gnomad AMR AF: 0.551

Gnomad ASJ AF: 0.565

Gnomad EAS AF: 0.244

Gnomad SAS AF: 0.410

Gnomad FIN AF: 0.718

Gnomad MID AF: 0.569

Gnomad NFE AF: 0.660

Gnomad OTH AF: 0.606

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

GnomAD4 genome AF: 0.589 AC: 85831 AN: 145790 Hom.: 25681 Cov.: 22 AF XY: 0.585 AC XY: 41435 AN XY: 70870

African (AFR) AF: 0.507 AC: 19635 AN: 38732

American (AMR) AF: 0.551 AC: 7912 AN: 14360

Ashkenazi Jewish (ASJ) AF: 0.565 AC: 1941 AN: 3436

East Asian (EAS) AF: 0.244 AC: 1129 AN: 4622

South Asian (SAS) AF: 0.410 AC: 1818 AN: 4436

European-Finnish (FIN) AF: 0.718 AC: 7198 AN: 10028

Middle Eastern (MID) AF: 0.574 AC: 162 AN: 282

European-Non Finnish (NFE) AF: 0.660 AC: 44168 AN: 66958

Other (OTH) AF: 0.601 AC: 1226 AN: 2040

Alfa AF: 0.620 Hom.: 36395

Bravo AF: 0.556

Asia WGS AF: 0.358 AC: 1244 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.11
DANN	Benign	0.58
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs9316567; hg19: chr13-22385730;