chr13-105130610-G-A

Variant names:

• chr13-105130610-G-A
• rs3916958
• ENST00000746226.1:n.142-6353C>T

Variant summary

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

The ENST00000746226.1(ENSG00000297213):​n.142-6353C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.55 in 151,708 control chromosomes in the GnomAD database, including 23,314 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 0.55 (23314 hom., cov: 31)
• Consequence: ENSG00000297213 ENST00000746226.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.677
• Publications: 1 publications found

Genes affected

ENSG00000297213 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.617 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
ENSG00000297213	ENST00000746226.1	n.142-6353C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.550 AC: 83408 AN: 151592 Hom.: 23297 Cov.: 31

Gnomad AFR AF: 0.623

Gnomad AMI AF: 0.572

Gnomad AMR AF: 0.463

Gnomad ASJ AF: 0.472

Gnomad EAS AF: 0.407

Gnomad SAS AF: 0.524

Gnomad FIN AF: 0.559

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.540

Gnomad OTH AF: 0.544

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

GnomAD4 genome AF: 0.550 AC: 83475 AN: 151708 Hom.: 23314 Cov.: 31 AF XY: 0.546 AC XY: 40469 AN XY: 74150

African (AFR) AF: 0.623 AC: 25770 AN: 41354

American (AMR) AF: 0.463 AC: 7044 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.472 AC: 1636 AN: 3464

East Asian (EAS) AF: 0.407 AC: 2095 AN: 5148

South Asian (SAS) AF: 0.525 AC: 2528 AN: 4814

European-Finnish (FIN) AF: 0.559 AC: 5883 AN: 10518

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.541 AC: 36690 AN: 67880

Other (OTH) AF: 0.547 AC: 1151 AN: 2104

Alfa AF: 0.535 Hom.: 60032

Bravo AF: 0.540

Asia WGS AF: 0.508 AC: 1761 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.89
DANN	Benign	0.70
PhyloP100		-0.68

Splicing

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

Other links and lift over

dbSNP: rs3916958; hg19: chr13-105782961;