rs947260

chr10-122769414-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_003570.2(DMBT1L1):n.746+59C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.528 in 152,360 control chromosomes in the GnomAD database, including 21,262 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 0.53 (21203 hom., cov: 31)
  • Exomes 𝑓: 0.55 (59 hom.)
• Consequence: DMBT1L1 NR_003570.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.207

Genes affected

DMBT1L1 (HGNC:49497): (deleted in malignant brain tumors 1 like 1 (pseudogene))

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.545 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DMBT1L1	NR_003570.2	n.746+59C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DMBT1L1	ENST00000439464.6	n.746+59C>T		intron_variant, non_coding_transcript_variant		2
DMBT1L1	ENST00000636837.3	n.1885+1034C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.528 AC: 80201 AN: 151808 Hom.: 21193 Cov.: 31

Gnomad AFR AF: 0.536

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.538

Gnomad ASJ AF: 0.456

Gnomad EAS AF: 0.433

Gnomad SAS AF: 0.565

Gnomad FIN AF: 0.528

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.532

Gnomad OTH AF: 0.548

GnomAD4 exome AF: 0.550 AC: 240 AN: 436 Hom.: 59 AF XY: 0.550 AC XY: 144 AN XY: 262

Gnomad4 FIN exome AF: 0.547

Gnomad4 NFE exome AF: 0.667

Gnomad4 OTH exome AF: 0.750

GnomAD4 genome AF: 0.528 AC: 80250 AN: 151924 Hom.: 21203 Cov.: 31 AF XY: 0.525 AC XY: 38940 AN XY: 74212

Gnomad4 AFR AF: 0.536

Gnomad4 AMR AF: 0.537

Gnomad4 ASJ AF: 0.456

Gnomad4 EAS AF: 0.433

Gnomad4 SAS AF: 0.563

Gnomad4 FIN AF: 0.528

Gnomad4 NFE AF: 0.532

Gnomad4 OTH AF: 0.547

Alfa AF: 0.531 Hom.: 28830

Bravo AF: 0.526

Asia WGS AF: 0.478 AC: 1665 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.42
Dann	Benign	0.17

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs947260; hg19: chr10-124528930;