rs1933331

Variant names:

• chr13-105648696-C-T
• rs1933331
• ENST00000831788.1:n.643-21154G>A

Variant summary

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

The ENST00000831788.1(ENSG00000308108):​n.643-21154G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0525 in 151,818 control chromosomes in the GnomAD database, including 562 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 0.053 (562 hom., cov: 32)
• Consequence: ENSG00000308108 ENST00000831788.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.363
• Publications: 3 publications found

Genes affected

ENSG00000308108 (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 (AFR) allele frequency at 95% confidence interval = 0.162 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370345	XR_007063935.1	n.674-6604G>A		intron_variant	Intron 5 of 6
LOC105370345	XR_931698.2	n.677-21154G>A		intron_variant	Intron 5 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000308108	ENST00000831788.1	n.643-21154G>A		intron_variant	Intron 5 of 6
ENSG00000308108	ENST00000831789.1	n.677-6604G>A		intron_variant	Intron 5 of 6

Frequencies

GnomAD3 genomes AF: 0.0523 AC: 7927 AN: 151702 Hom.: 549 Cov.: 32

Gnomad AFR AF: 0.165

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0293

Gnomad ASJ AF: 0.00749

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000830

Gnomad FIN AF: 0.000380

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.00790

Gnomad OTH AF: 0.0478

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

GnomAD4 genome AF: 0.0525 AC: 7972 AN: 151818 Hom.: 562 Cov.: 32 AF XY: 0.0513 AC XY: 3807 AN XY: 74174

African (AFR) AF: 0.165 AC: 6837 AN: 41374

American (AMR) AF: 0.0293 AC: 446 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.00749 AC: 26 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5156

South Asian (SAS) AF: 0.000831 AC: 4 AN: 4814

European-Finnish (FIN) AF: 0.000380 AC: 4 AN: 10528

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.00790 AC: 537 AN: 67940

Other (OTH) AF: 0.0473 AC: 100 AN: 2112

Alfa AF: 0.0238 Hom.: 605

Bravo AF: 0.0590

Asia WGS AF: 0.0170 AC: 59 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	2.0
DANN	Benign	0.41
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs1933331; hg19: chr13-106301045;