rs7916571

chr10-122792263-T-Achr10-122792263-T-C

Variant summary

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

The NR_003570.2(DMBT1L1):n.2774-24T>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.614 in 152,402 control chromosomes in the GnomAD database, including 28,876 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 0.61 (28775 hom., cov: 31)
  • Exomes 𝑓: 0.69 (101 hom.)
• Consequence: DMBT1L1 NR_003570.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.90

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=-0.86).
• 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	UniProt
DMBT1L1	NR_003570.2	n.2774-24T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DMBT1L1	ENST00000439464.6	n.2774-24T>A		intron_variant, non_coding_transcript_variant		2
DMBT1L1	ENST00000636837.3	n.3615-24T>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.614 AC: 93255 AN: 151856 Hom.: 28769 Cov.: 31

Gnomad AFR AF: 0.534

Gnomad AMI AF: 0.609

Gnomad AMR AF: 0.626

Gnomad ASJ AF: 0.625

Gnomad EAS AF: 0.552

Gnomad SAS AF: 0.732

Gnomad FIN AF: 0.638

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.652

Gnomad OTH AF: 0.616

GnomAD4 exome AF: 0.689 AC: 295 AN: 428 Hom.: 101 Cov.: 0 AF XY: 0.695 AC XY: 178 AN XY: 256

Gnomad4 FIN exome AF: 0.690

Gnomad4 NFE exome AF: 0.500

Gnomad4 OTH exome AF: 0.667

GnomAD4 genome AF: 0.614 AC: 93298 AN: 151974 Hom.: 28775 Cov.: 31 AF XY: 0.616 AC XY: 45725 AN XY: 74282

Gnomad4 AFR AF: 0.533

Gnomad4 AMR AF: 0.626

Gnomad4 ASJ AF: 0.625

Gnomad4 EAS AF: 0.551

Gnomad4 SAS AF: 0.732

Gnomad4 FIN AF: 0.638

Gnomad4 NFE AF: 0.652

Gnomad4 OTH AF: 0.617

Alfa AF: 0.456 Hom.: 1002

Bravo AF: 0.606

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	0.025
Dann	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7916571; hg19: chr10-124551779; COSMIC: COSV71563453;