10-122815857-T-C

Variant names:

• chr10-122815857-T-C
• rs7895725
• XM_047426130.1:c.368-2751T>C

Variant summary

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

The ENST00000636837.3(DMBT1L1):​n.4629-2751T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.762 in 152,092 control chromosomes in the GnomAD database, including 44,352 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 0.76 (44352 hom., cov: 32)
• Consequence: DMBT1L1 ENST00000636837.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.970
• Publications: 4 publications found

Genes affected

LOC124900290 (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=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.812 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DMBT1L1	ENST00000636837.3	TSL:6	n.4629-2751T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.762 AC: 115874 AN: 151972 Hom.: 44320 Cov.: 32

Gnomad AFR AF: 0.815

Gnomad AMI AF: 0.695

Gnomad AMR AF: 0.717

Gnomad ASJ AF: 0.773

Gnomad EAS AF: 0.594

Gnomad SAS AF: 0.833

Gnomad FIN AF: 0.717

Gnomad MID AF: 0.842

Gnomad NFE AF: 0.756

Gnomad OTH AF: 0.763

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

GnomAD4 genome AF: 0.762 AC: 115958 AN: 152092 Hom.: 44352 Cov.: 32 AF XY: 0.760 AC XY: 56536 AN XY: 74342

African (AFR) AF: 0.814 AC: 33783 AN: 41486

American (AMR) AF: 0.717 AC: 10962 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.773 AC: 2681 AN: 3468

East Asian (EAS) AF: 0.593 AC: 3059 AN: 5156

South Asian (SAS) AF: 0.833 AC: 4013 AN: 4816

European-Finnish (FIN) AF: 0.717 AC: 7577 AN: 10568

Middle Eastern (MID) AF: 0.833 AC: 245 AN: 294

European-Non Finnish (NFE) AF: 0.756 AC: 51389 AN: 67994

Other (OTH) AF: 0.765 AC: 1615 AN: 2112

Alfa AF: 0.755 Hom.: 19474

Bravo AF: 0.762

Asia WGS AF: 0.716 AC: 2493 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.19
DANN	Benign	0.36
PhyloP100		-0.97

Splicing

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

Other links and lift over

dbSNP: rs7895725; hg19: chr10-124575373;