chr13-104869384-A-T

Variant names:

• chr13-104869384-A-T
• rs3916951
• ENST00000841827.1:n.164+1646A>T

Variant summary

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

The ENST00000841827.1(ENSG00000309518):​n.164+1646A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.344 in 152,012 control chromosomes in the GnomAD database, including 9,297 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 0.34 (9297 hom., cov: 32)
• Consequence: ENSG00000309518 ENST00000841827.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.876
• Publications: 1 publications found

Genes affected

ENSG00000309518 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.475 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107984608	XR_001749997.2	n.128-20913A>T		intron_variant	Intron 1 of 2
LOC105370342	XR_931691.3	n.*220A>T		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000309518	ENST00000841827.1	n.164+1646A>T		intron_variant	Intron 1 of 1
ENSG00000309518	ENST00000841828.1	n.242+215A>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.343 AC: 52162 AN: 151894 Hom.: 9281 Cov.: 32

Gnomad AFR AF: 0.414

Gnomad AMI AF: 0.300

Gnomad AMR AF: 0.304

Gnomad ASJ AF: 0.223

Gnomad EAS AF: 0.490

Gnomad SAS AF: 0.376

Gnomad FIN AF: 0.335

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.305

Gnomad OTH AF: 0.301

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

GnomAD4 genome AF: 0.344 AC: 52220 AN: 152012 Hom.: 9297 Cov.: 32 AF XY: 0.345 AC XY: 25655 AN XY: 74290

African (AFR) AF: 0.414 AC: 17186 AN: 41474

American (AMR) AF: 0.303 AC: 4631 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.223 AC: 773 AN: 3466

East Asian (EAS) AF: 0.491 AC: 2530 AN: 5152

South Asian (SAS) AF: 0.375 AC: 1807 AN: 4816

European-Finnish (FIN) AF: 0.335 AC: 3538 AN: 10554

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.305 AC: 20747 AN: 67972

Other (OTH) AF: 0.304 AC: 641 AN: 2112

Alfa AF: 0.328 Hom.: 1078

Bravo AF: 0.344

Asia WGS AF: 0.408 AC: 1420 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.3
DANN	Benign	0.35
PhyloP100		0.88

Splicing

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

Other links and lift over

dbSNP: rs3916951; hg19: chr13-105521735;