rs1381632

Variant names:

• chr4-87647832-T-A
• rs1381632
• ENST00000506480.5:n.322+25158A>T

Variant summary

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

The ENST00000506480.5(ENSG00000249001):​n.322+25158A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.173 in 152,172 control chromosomes in the GnomAD database, including 2,697 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 0.17 (2697 hom., cov: 32)
• Consequence: ENSG00000249001 ENST00000506480.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.492
• Publications: 5 publications found

Genes affected

ENSG00000249001 (HGNC:58144):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.248 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DMP1-AS1	NR_198971.1	n.366+25158A>T		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000249001	ENST00000506480.5	n.322+25158A>T		intron_variant	Intron 3 of 3	3
ENSG00000249001	ENST00000829286.1	n.356+25158A>T		intron_variant	Intron 3 of 3
ENSG00000249001	ENST00000829287.1	n.348+25158A>T		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.173 AC: 26364 AN: 152054 Hom.: 2699 Cov.: 32

Gnomad AFR AF: 0.0752

Gnomad AMI AF: 0.172

Gnomad AMR AF: 0.254

Gnomad ASJ AF: 0.244

Gnomad EAS AF: 0.206

Gnomad SAS AF: 0.128

Gnomad FIN AF: 0.151

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.214

Gnomad OTH AF: 0.208

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

GnomAD4 genome AF: 0.173 AC: 26370 AN: 152172 Hom.: 2697 Cov.: 32 AF XY: 0.172 AC XY: 12776 AN XY: 74394

African (AFR) AF: 0.0752 AC: 3126 AN: 41562

American (AMR) AF: 0.254 AC: 3885 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.244 AC: 845 AN: 3468

East Asian (EAS) AF: 0.206 AC: 1069 AN: 5178

South Asian (SAS) AF: 0.128 AC: 617 AN: 4826

European-Finnish (FIN) AF: 0.151 AC: 1597 AN: 10580

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.214 AC: 14548 AN: 67962

Other (OTH) AF: 0.208 AC: 440 AN: 2114

Alfa AF: 0.193 Hom.: 379

Bravo AF: 0.178

Asia WGS AF: 0.146 AC: 515 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.2
DANN	Benign	0.74
PhyloP100		0.49

Splicing

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

Other links and lift over

dbSNP: rs1381632; hg19: chr4-88568984;