chr10-122777744-C-T

Position:

• chr10-122777744-C-T

Variant summary

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

The ENST00000439464.6(DMBT1L1):​n.1239C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.577 in 153,238 control chromosomes in the GnomAD database, including 25,600 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 0.58 (25362 hom., cov: 33)
  • Exomes 𝑓: 0.63 (238 hom.)
• Consequence: DMBT1L1 ENST00000439464.6 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.822

Genes affected

DMBT1L1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.5).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.712 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DMBT1L1	NR_003570.2	n.1239C>T		non_coding_transcript_exon_variant	14/28

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DMBT1L1	ENST00000439464.6	n.1239C>T		non_coding_transcript_exon_variant	14/28	2
DMBT1L1	ENST00000636837.3	n.2234C>T		non_coding_transcript_exon_variant	9/24	6

Frequencies

GnomAD3 genomes AF: 0.577 AC: 87705 AN: 151972 Hom.: 25353 Cov.: 33

Gnomad AFR AF: 0.518

Gnomad AMI AF: 0.455

Gnomad AMR AF: 0.602

Gnomad ASJ AF: 0.618

Gnomad EAS AF: 0.554

Gnomad SAS AF: 0.732

Gnomad FIN AF: 0.547

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.602

Gnomad OTH AF: 0.589

GnomAD4 exome AF: 0.625 AC: 719 AN: 1150 Hom.: 238 Cov.: 0 AF XY: 0.625 AC XY: 519 AN XY: 830

Gnomad4 AFR exome AF: 0.600

Gnomad4 AMR exome AF: 0.714

Gnomad4 ASJ exome AF: 0.500

Gnomad4 EAS exome AF: 0.500

Gnomad4 SAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.569

Gnomad4 NFE exome AF: 0.670

Gnomad4 OTH exome AF: 0.739

GnomAD4 genome AF: 0.577 AC: 87750 AN: 152088 Hom.: 25362 Cov.: 33 AF XY: 0.579 AC XY: 43016 AN XY: 74352

Gnomad4 AFR AF: 0.517

Gnomad4 AMR AF: 0.602

Gnomad4 ASJ AF: 0.618

Gnomad4 EAS AF: 0.553

Gnomad4 SAS AF: 0.732

Gnomad4 FIN AF: 0.547

Gnomad4 NFE AF: 0.602

Gnomad4 OTH AF: 0.591

Alfa AF: 0.518 Hom.: 2249

Bravo AF: 0.574

Asia WGS AF: 0.648 AC: 2258 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.50
CADD	Benign	13
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2421131; hg19: chr10-124537260;