chr10-122780202-G-T

Position:

• chr10-122780202-G-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000439464.6(DMBT1L1):​n.1720G>T variant causes a non coding transcript exon change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.621 in 152,886 control chromosomes in the GnomAD database, including 29,710 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 0.62 (29553 hom., cov: 33)
  • Exomes 𝑓: 0.63 (157 hom.)
• Consequence: DMBT1L1 ENST00000439464.6 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 7.87

Genes affected

DMBT1L1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.4).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.719 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DMBT1L1	NR_003570.2	n.1720G>T		non_coding_transcript_exon_variant	16/28

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DMBT1L1	ENST00000439464.6	n.1720G>T		non_coding_transcript_exon_variant	16/28	2
DMBT1L1	ENST00000636837.3	n.2685G>T		non_coding_transcript_exon_variant	10/24	6

Frequencies

GnomAD3 genomes AF: 0.622 AC: 94469 AN: 151994 Hom.: 29545 Cov.: 33

Gnomad AFR AF: 0.528

Gnomad AMI AF: 0.612

Gnomad AMR AF: 0.635

Gnomad ASJ AF: 0.638

Gnomad EAS AF: 0.552

Gnomad SAS AF: 0.740

Gnomad FIN AF: 0.650

Gnomad MID AF: 0.706

Gnomad NFE AF: 0.667

Gnomad OTH AF: 0.626

GnomAD4 exome AF: 0.631 AC: 487 AN: 772 Hom.: 157 Cov.: 0 AF XY: 0.635 AC XY: 316 AN XY: 498

Gnomad4 AFR exome AF: 0.500

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.667

Gnomad4 EAS exome AF: 0.750

Gnomad4 SAS exome AF: 0.750

Gnomad4 FIN exome AF: 0.686

Gnomad4 NFE exome AF: 0.552

Gnomad4 OTH exome AF: 0.650

GnomAD4 genome AF: 0.621 AC: 94513 AN: 152114 Hom.: 29553 Cov.: 33 AF XY: 0.623 AC XY: 46318 AN XY: 74336

Gnomad4 AFR AF: 0.527

Gnomad4 AMR AF: 0.635

Gnomad4 ASJ AF: 0.638

Gnomad4 EAS AF: 0.551

Gnomad4 SAS AF: 0.740

Gnomad4 FIN AF: 0.650

Gnomad4 NFE AF: 0.667

Gnomad4 OTH AF: 0.627

Alfa AF: 0.658 Hom.: 39104

Bravo AF: 0.613

Asia WGS AF: 0.650 AC: 2264 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.40
CADD	Benign	15
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1970473; hg19: chr10-124539718;