rs10794613

Positions:

• chr10-122754622-C-G
• chr10-122754622-C-T

Variant summary

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

The ENST00000636837.3(DMBT1L1):​n.954-2084C>G 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 0.208 in 152,110 control chromosomes in the GnomAD database, including 3,875 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 0.21 (3875 hom., cov: 32)
• Consequence: DMBT1L1 ENST00000636837.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0280

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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.542 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DMBT1L1	ENST00000636837.3	n.954-2084C>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.208 AC: 31559 AN: 151992 Hom.: 3878 Cov.: 32

Gnomad AFR AF: 0.128

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.274

Gnomad ASJ AF: 0.155

Gnomad EAS AF: 0.559

Gnomad SAS AF: 0.347

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.255

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.208

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

GnomAD4 genome AF: 0.208 AC: 31578 AN: 152110 Hom.: 3875 Cov.: 32 AF XY: 0.214 AC XY: 15894 AN XY: 74348

Gnomad4 AFR AF: 0.128

Gnomad4 AMR AF: 0.274

Gnomad4 ASJ AF: 0.155

Gnomad4 EAS AF: 0.559

Gnomad4 SAS AF: 0.348

Gnomad4 FIN AF: 0.197

Gnomad4 NFE AF: 0.209

Gnomad4 OTH AF: 0.211

Alfa AF: 0.125 Hom.: 214

Bravo AF: 0.212

Asia WGS AF: 0.429 AC: 1492 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.1
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: rs10794613; hg19: chr10-124514138;