rs10902963

Variant names:

• chr10-122785058-C-T
• rs10902963
• ENST00000439464.6:n.2136C>T

Variant summary

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

The ENST00000439464.6(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 ENST00000439464.6 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.239
• Publications: 5 publications found

Genes affected

DMBT1L1 (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
DMBT1L1	NR_003570.2	n.2136C>T		non_coding_transcript_exon_variant	Exon 20 of 28

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DMBT1L1	ENST00000439464.6	n.2136C>T		non_coding_transcript_exon_variant	Exon 20 of 28	2
DMBT1L1	ENST00000636837.3	n.3078+587C>T		intron_variant	Intron 13 of 23	6

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.00 AC: 0 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.123 AC: 5101 AN: 41520

American (AMR) AF: 0.0310 AC: 474 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.00317 AC: 11 AN: 3468

East Asian (EAS) AF: 0.112 AC: 579 AN: 5184

South Asian (SAS) AF: 0.0184 AC: 89 AN: 4828

European-Finnish (FIN) AF: 0.0101 AC: 107 AN: 10590

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.0178 AC: 1211 AN: 68006

Other (OTH) AF: 0.0359 AC: 76 AN: 2116

Alfa AF: 0.0276 Hom.: 236

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
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs10902963; hg19: chr10-124544574;