10-122815857-T-C

Variant summary

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

The XM_047426130.1(LOC124900290):c.368-2751T>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: LOC124900290 XM_047426130.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.970

Genes affected

LOC124900290 (HGNC:):

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=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.812 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124900290	XM_047426130.1	c.368-2751T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DMBT1L1	ENST00000636837.3	n.4629-2751T>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.814

Gnomad4 AMR AF: 0.717

Gnomad4 ASJ AF: 0.773

Gnomad4 EAS AF: 0.593

Gnomad4 SAS AF: 0.833

Gnomad4 FIN AF: 0.717

Gnomad4 NFE AF: 0.756

Gnomad4 OTH AF: 0.765

Alfa AF: 0.754 Hom.: 16975

Bravo AF: 0.762

Asia WGS AF: 0.716 AC: 2493 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.19
Dann	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7895725; hg19: chr10-124575373;