chr13-104807897-A-G

Variant names:

• chr13-104807897-A-G
• rs873330
• ENST00000807560.1:n.412-2279T>C

Variant summary

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

The ENST00000807560.1(ENSG00000304988):​n.412-2279T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.312 in 152,086 control chromosomes in the GnomAD database, including 8,727 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 0.31 (8727 hom., cov: 33)
• Consequence: ENSG00000304988 ENST00000807560.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.830
• Publications: 1 publications found

Genes affected

ENSG00000304988 (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 (SAS) allele frequency at 95% confidence interval = 0.458 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107984606	XR_001749993.2	n.422-2279T>C		intron_variant	Intron 3 of 3
LOC107984606	XR_001749994.2	n.297-2279T>C		intron_variant	Intron 2 of 2
LOC107984606	XR_001749995.2	n.296+29306T>C		intron_variant	Intron 2 of 3
LOC107984606	XR_007063859.1	n.421+15766T>C		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000304988	ENST00000807560.1	n.412-2279T>C		intron_variant	Intron 3 of 3
ENSG00000304988	ENST00000807561.1	n.239-2279T>C		intron_variant	Intron 2 of 2
ENSG00000304988	ENST00000807562.1	n.321-2279T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.312 AC: 47432 AN: 151968 Hom.: 8732 Cov.: 33

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.338

Gnomad AMR AF: 0.333

Gnomad ASJ AF: 0.361

Gnomad EAS AF: 0.265

Gnomad SAS AF: 0.475

Gnomad FIN AF: 0.409

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.406

Gnomad OTH AF: 0.300

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

GnomAD4 genome AF: 0.312 AC: 47420 AN: 152086 Hom.: 8727 Cov.: 33 AF XY: 0.315 AC XY: 23448 AN XY: 74344

African (AFR) AF: 0.108 AC: 4488 AN: 41530

American (AMR) AF: 0.332 AC: 5067 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.361 AC: 1253 AN: 3468

East Asian (EAS) AF: 0.265 AC: 1368 AN: 5172

South Asian (SAS) AF: 0.475 AC: 2286 AN: 4816

European-Finnish (FIN) AF: 0.409 AC: 4322 AN: 10574

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.406 AC: 27587 AN: 67966

Other (OTH) AF: 0.297 AC: 627 AN: 2112

Alfa AF: 0.276 Hom.: 2804

Bravo AF: 0.292

Asia WGS AF: 0.335 AC: 1166 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	1.7
DANN	Benign	0.60
PhyloP100		-0.83

Splicing

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

Other links and lift over

dbSNP: rs873330; hg19: chr13-105460248;