rs1328949

Variant names:

• chr13-31442296-A-G
• rs1328949
• ENST00000843719.1:n.220-24539A>G

Your query was ambiguous. Multiple possible variants found:

• chr13-31442296-A-G
• chr13-31442296-A-T

Variant summary

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

The ENST00000843719.1(ENSG00000278305):​n.220-24539A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.366 in 152,052 control chromosomes in the GnomAD database, including 10,547 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 0.37 (10547 hom., cov: 32)
• Consequence: ENSG00000278305 ENST00000843719.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.68
• Publications: 2 publications found

Genes affected

ENSG00000278305 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.56).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.46 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370150	XR_001749806.1	n.360-1069A>G		intron_variant	Intron 1 of 3
LOC105370150	XR_941829.1	n.232-1069A>G		intron_variant	Intron 3 of 5
LOC105370150	XR_941830.1	n.234-1069A>G		intron_variant	Intron 3 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000278305	ENST00000843719.1	n.220-24539A>G		intron_variant	Intron 1 of 3
ENSG00000278305	ENST00000843720.1	n.488-1069A>G		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.365 AC: 55478 AN: 151932 Hom.: 10505 Cov.: 32

Gnomad AFR AF: 0.465

Gnomad AMI AF: 0.160

Gnomad AMR AF: 0.365

Gnomad ASJ AF: 0.275

Gnomad EAS AF: 0.302

Gnomad SAS AF: 0.368

Gnomad FIN AF: 0.352

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.319

Gnomad OTH AF: 0.337

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

GnomAD4 genome AF: 0.366 AC: 55580 AN: 152052 Hom.: 10547 Cov.: 32 AF XY: 0.368 AC XY: 27369 AN XY: 74322

African (AFR) AF: 0.466 AC: 19314 AN: 41464

American (AMR) AF: 0.366 AC: 5587 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.275 AC: 952 AN: 3468

East Asian (EAS) AF: 0.302 AC: 1553 AN: 5146

South Asian (SAS) AF: 0.368 AC: 1771 AN: 4812

European-Finnish (FIN) AF: 0.352 AC: 3728 AN: 10580

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.319 AC: 21718 AN: 67986

Other (OTH) AF: 0.342 AC: 723 AN: 2112

Alfa AF: 0.326 Hom.: 4349

Bravo AF: 0.370

Asia WGS AF: 0.391 AC: 1361 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
CADD	Benign	15
DANN	Benign	0.85
PhyloP100		1.7

Splicing

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

Other links and lift over

dbSNP: rs1328949; hg19: chr13-32016433;