10-122736447-A-T

Position:

• chr10-122736447-A-T

Variant summary

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

The ENST00000636837.3(DMBT1L1):​n.630+1787A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.394 in 151,950 control chromosomes in the GnomAD database, including 12,502 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 0.39 (12502 hom., cov: 32)
• Consequence: DMBT1L1 ENST00000636837.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.27

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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.509 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DMBT1L1	ENST00000636837.3	n.630+1787A>T		intron_variant	Intron 2 of 23	6

Frequencies

GnomAD3 genomes AF: 0.394 AC: 59838 AN: 151832 Hom.: 12457 Cov.: 32

Gnomad AFR AF: 0.514

Gnomad AMI AF: 0.422

Gnomad AMR AF: 0.429

Gnomad ASJ AF: 0.391

Gnomad EAS AF: 0.512

Gnomad SAS AF: 0.440

Gnomad FIN AF: 0.270

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.320

Gnomad OTH AF: 0.400

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

GnomAD4 genome AF: 0.394 AC: 59931 AN: 151950 Hom.: 12502 Cov.: 32 AF XY: 0.395 AC XY: 29304 AN XY: 74264

Gnomad4 AFR AF: 0.515

Gnomad4 AMR AF: 0.429

Gnomad4 ASJ AF: 0.391

Gnomad4 EAS AF: 0.513

Gnomad4 SAS AF: 0.439

Gnomad4 FIN AF: 0.270

Gnomad4 NFE AF: 0.320

Gnomad4 OTH AF: 0.398

Alfa AF: 0.362 Hom.: 1318

Bravo AF: 0.411

Asia WGS AF: 0.464 AC: 1609 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.065
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2421125; hg19: chr10-124495963;