chr13-46924501-A-G

Variant names:

• chr13-46924501-A-G
• rs943903
• ENST00000778995.1:n.111+31958A>G

Variant summary

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

The ENST00000778995.1(ENSG00000301465):​n.111+31958A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.294 in 151,974 control chromosomes in the GnomAD database, including 6,799 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 0.29 (6799 hom., cov: 32)
• Consequence: ENSG00000301465 ENST00000778995.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.741
• Publications: 1 publications found

Genes affected

ENSG00000301465 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.349 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
ENSG00000301465	ENST00000778995.1	n.111+31958A>G		intron_variant	Intron 1 of 1
ENSG00000301465	ENST00000778996.1	n.122+31897A>G		intron_variant	Intron 1 of 1
ENSG00000301465	ENST00000778997.1	n.120+28757A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.294 AC: 44611 AN: 151856 Hom.: 6790 Cov.: 32

Gnomad AFR AF: 0.354

Gnomad AMI AF: 0.271

Gnomad AMR AF: 0.227

Gnomad ASJ AF: 0.221

Gnomad EAS AF: 0.0761

Gnomad SAS AF: 0.261

Gnomad FIN AF: 0.289

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.296

Gnomad OTH AF: 0.282

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

GnomAD4 genome AF: 0.294 AC: 44653 AN: 151974 Hom.: 6799 Cov.: 32 AF XY: 0.291 AC XY: 21627 AN XY: 74278

African (AFR) AF: 0.354 AC: 14664 AN: 41422

American (AMR) AF: 0.227 AC: 3470 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.221 AC: 767 AN: 3470

East Asian (EAS) AF: 0.0765 AC: 395 AN: 5166

South Asian (SAS) AF: 0.261 AC: 1258 AN: 4820

European-Finnish (FIN) AF: 0.289 AC: 3054 AN: 10552

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.296 AC: 20129 AN: 67942

Other (OTH) AF: 0.278 AC: 589 AN: 2116

Alfa AF: 0.295 Hom.: 3438

Bravo AF: 0.291

Asia WGS AF: 0.156 AC: 545 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.59
DANN	Benign	0.38
PhyloP100		-0.74

Splicing

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

Other links and lift over

dbSNP: rs943903; hg19: chr13-47498636;