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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000843719.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000278305	ENST00000843719.1		n.220-24539A>G		intron	N/A
	ENSG00000278305	ENST00000843720.1		n.488-1069A>G		intron	N/A

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 v4.9

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;