rs10902963

Positions:

• chr10-122785058-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.2136C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0505 in 152,202 control chromosomes in the GnomAD database, including 403 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 0.050 (403 hom., cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: DMBT1L1 NR_003570.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.239

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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.12 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DMBT1L1	NR_003570.2	n.2136C>T		non_coding_transcript_exon_variant	20/28

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DMBT1L1	ENST00000439464.6	n.2136C>T		non_coding_transcript_exon_variant	20/28	2
DMBT1L1	ENST00000636837.3	n.3078+587C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0502 AC: 7639 AN: 152084 Hom.: 391 Cov.: 33

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.0417

Gnomad AMR AF: 0.0310

Gnomad ASJ AF: 0.00317

Gnomad EAS AF: 0.112

Gnomad SAS AF: 0.0184

Gnomad FIN AF: 0.0101

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0178

Gnomad OTH AF: 0.0363

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

Gnomad4 EAS exome AF: 0.00

GnomAD4 genome AF: 0.0505 AC: 7686 AN: 152202 Hom.: 403 Cov.: 33 AF XY: 0.0493 AC XY: 3671 AN XY: 74420

Gnomad4 AFR AF: 0.123

Gnomad4 AMR AF: 0.0310

Gnomad4 ASJ AF: 0.00317

Gnomad4 EAS AF: 0.112

Gnomad4 SAS AF: 0.0184

Gnomad4 FIN AF: 0.0101

Gnomad4 NFE AF: 0.0178

Gnomad4 OTH AF: 0.0359

Alfa AF: 0.0241 Hom.: 141

Bravo AF: 0.0557

Asia WGS AF: 0.0710 AC: 245 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	5.5
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10902963; hg19: chr10-124544574;