rs538385

Variant names:

• chr13-29655528-T-C
• rs538385
• ENST00000728647.1:n.514-3T>C

Variant summary

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

The ENST00000728647.1(ENSG00000295213):​n.514-3T>C variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.371 in 151,986 control chromosomes in the GnomAD database, including 10,877 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 (10877 hom., cov: 32)
• Consequence: ENSG00000295213 ENST00000728647.1 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.912
• Publications: 5 publications found

Genes affected

ENSG00000295213 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.455 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000728647.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC102723345	NR_135320.1		n.*50T>C		downstream_gene	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000295213	ENST00000728647.1		n.514-3T>C		splice_region intron	N/A
	ENSG00000295213	ENST00000728648.1		n.324-3T>C		splice_region intron	N/A
	ENSG00000295213	ENST00000728649.1		n.599-3T>C		splice_region intron	N/A

Frequencies

GnomAD3 genomes AF: 0.371 AC: 56351 AN: 151868 Hom.: 10860 Cov.: 32

Gnomad AFR AF: 0.297

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.463

Gnomad ASJ AF: 0.461

Gnomad EAS AF: 0.343

Gnomad SAS AF: 0.469

Gnomad FIN AF: 0.398

Gnomad MID AF: 0.436

Gnomad NFE AF: 0.383

Gnomad OTH AF: 0.400

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

GnomAD4 genome AF: 0.371 AC: 56382 AN: 151986 Hom.: 10877 Cov.: 32 AF XY: 0.376 AC XY: 27918 AN XY: 74298

African (AFR) AF: 0.297 AC: 12312 AN: 41458

American (AMR) AF: 0.464 AC: 7074 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.461 AC: 1596 AN: 3462

East Asian (EAS) AF: 0.342 AC: 1765 AN: 5158

South Asian (SAS) AF: 0.469 AC: 2261 AN: 4826

European-Finnish (FIN) AF: 0.398 AC: 4197 AN: 10548

Middle Eastern (MID) AF: 0.435 AC: 127 AN: 292

European-Non Finnish (NFE) AF: 0.383 AC: 26028 AN: 67960

Other (OTH) AF: 0.396 AC: 838 AN: 2114

Alfa AF: 0.386 Hom.: 33607

Bravo AF: 0.372

Asia WGS AF: 0.371 AC: 1293 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.072
DANN	Benign	0.35
PhyloP100		-0.91

Splicing

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

Other links and lift over

dbSNP: rs538385; hg19: chr13-30229665;