10-122780202-G-T

Variant names:

• chr10-122780202-G-T
• rs1970473
• ENST00000439464.6:n.1720G>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

Genes affected

DMBT1L1 (HGNC:):

DMBT1L1 (HGNC:49497): (deleted in malignant brain tumors 1 like 1 (pseudogene))

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000439464.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DMBT1L1	NR_003570.2		n.1720G>T		non_coding_transcript_exon	Exon 16 of 28

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DMBT1L1	ENST00000439464.6	TSL:2	n.1720G>T		non_coding_transcript_exon	Exon 16 of 28
	DMBT1L1	ENST00000636837.3	TSL:6	n.2685G>T		non_coding_transcript_exon	Exon 10 of 24

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

African (AFR) AF: 0.500 AC: 3 AN: 6

American (AMR) AF: 0.00 AC: 0 AN: 2

Ashkenazi Jewish (ASJ) AF: 0.667 AC: 4 AN: 6

East Asian (EAS) AF: 0.750 AC: 3 AN: 4

South Asian (SAS) AF: 0.750 AC: 3 AN: 4

European-Finnish (FIN) AF: 0.686 AC: 303 AN: 442

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.552 AC: 158 AN: 286

Other (OTH) AF: 0.650 AC: 13 AN: 20

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

African (AFR) AF: 0.527 AC: 21874 AN: 41502

American (AMR) AF: 0.635 AC: 9709 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.638 AC: 2215 AN: 3472

East Asian (EAS) AF: 0.551 AC: 2832 AN: 5144

South Asian (SAS) AF: 0.740 AC: 3568 AN: 4824

European-Finnish (FIN) AF: 0.650 AC: 6897 AN: 10606

Middle Eastern (MID) AF: 0.718 AC: 211 AN: 294

European-Non Finnish (NFE) AF: 0.667 AC: 45325 AN: 67966

Other (OTH) AF: 0.627 AC: 1326 AN: 2114

Alfa AF: 0.653 Hom.: 48937

Bravo AF: 0.613

Asia WGS AF: 0.650 AC: 2264 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.40
CADD	Benign	15
DANN	Benign	0.66
PhyloP100		7.9

Splicing

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

Other links and lift over

dbSNP: rs1970473; hg19: chr10-124539718;