13-99416013-C-T

Variant names:

• chr13-99416013-C-T
• rs9557217
• ENST00000642991.1:n.168+1044G>A

Variant summary

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

The ENST00000642991.1(ENSG00000290577):​n.168+1044G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.634 in 152,106 control chromosomes in the GnomAD database, including 32,268 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 0.63 (32268 hom., cov: 32)
• Consequence: ENSG00000290577 ENST00000642991.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.117
• Publications: 6 publications found

Genes affected

ENSG00000290577 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.743 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
ENSG00000290577	ENST00000642991.1	n.168+1044G>A		intron_variant	Intron 1 of 1
ENSG00000290577	ENST00000834577.1	n.133+719G>A		intron_variant	Intron 1 of 1
ENSG00000290577	ENST00000834579.1	n.*127G>A		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.635 AC: 96498 AN: 151988 Hom.: 32272 Cov.: 32

Gnomad AFR AF: 0.412

Gnomad AMI AF: 0.794

Gnomad AMR AF: 0.645

Gnomad ASJ AF: 0.778

Gnomad EAS AF: 0.621

Gnomad SAS AF: 0.694

Gnomad FIN AF: 0.672

Gnomad MID AF: 0.772

Gnomad NFE AF: 0.748

Gnomad OTH AF: 0.667

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

GnomAD4 genome AF: 0.634 AC: 96511 AN: 152106 Hom.: 32268 Cov.: 32 AF XY: 0.634 AC XY: 47115 AN XY: 74370

African (AFR) AF: 0.411 AC: 17066 AN: 41476

American (AMR) AF: 0.644 AC: 9843 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.778 AC: 2699 AN: 3468

East Asian (EAS) AF: 0.621 AC: 3210 AN: 5168

South Asian (SAS) AF: 0.698 AC: 3370 AN: 4830

European-Finnish (FIN) AF: 0.672 AC: 7105 AN: 10572

Middle Eastern (MID) AF: 0.765 AC: 225 AN: 294

European-Non Finnish (NFE) AF: 0.748 AC: 50870 AN: 67988

Other (OTH) AF: 0.661 AC: 1399 AN: 2116

Alfa AF: 0.721 Hom.: 23527

Bravo AF: 0.625

Asia WGS AF: 0.606 AC: 2110 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.1
DANN	Benign	0.87
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs9557217; hg19: chr13-100068267;