ENST00000636837.3:n.954-2084C>G

Variant names:

• chr10-122754622-C-G
• rs10794613
• ENST00000636837.3:n.954-2084C>G

Variant summary

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

The ENST00000636837.3(DMBT1L1):​n.954-2084C>G variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0280
• Publications: 4 publications found

Genes affected

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

DMBT1L1 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000636837.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DMBT1L1	ENST00000636837.3	TSL:6	n.954-2084C>G		intron	N/A
	DMBT1L1	ENST00000832350.1		n.310+1015C>G		intron	N/A

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

African (AFR) AF: 0.128 AC: 5296 AN: 41512

American (AMR) AF: 0.274 AC: 4193 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.155 AC: 538 AN: 3464

East Asian (EAS) AF: 0.559 AC: 2889 AN: 5168

South Asian (SAS) AF: 0.348 AC: 1674 AN: 4812

European-Finnish (FIN) AF: 0.197 AC: 2086 AN: 10572

Middle Eastern (MID) AF: 0.260 AC: 76 AN: 292

European-Non Finnish (NFE) AF: 0.209 AC: 14242 AN: 67988

Other (OTH) AF: 0.211 AC: 443 AN: 2104

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.1
DANN	Benign	0.62
PhyloP100		-0.028

Splicing

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

Other links and lift over

dbSNP: rs10794613; hg19: chr10-124514138;