rs947260

Variant names:

• chr10-122769414-C-T
• rs947260
• ENST00000439464.6:n.746+59C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000439464.6(DMBT1L1):​n.746+59C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.528 in 152,360 control chromosomes in the GnomAD database, including 21,262 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 0.53 (21203 hom., cov: 31)
  • Exomes 𝑓: 0.55 (59 hom.)
• Consequence: DMBT1L1 ENST00000439464.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.207
• Publications: 4 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.545 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.746+59C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DMBT1L1	ENST00000439464.6	TSL:2	n.746+59C>T		intron	N/A
	DMBT1L1	ENST00000636837.3	TSL:6	n.1885+1034C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.528 AC: 80201 AN: 151808 Hom.: 21193 Cov.: 31

Gnomad AFR AF: 0.536

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.538

Gnomad ASJ AF: 0.456

Gnomad EAS AF: 0.433

Gnomad SAS AF: 0.565

Gnomad FIN AF: 0.528

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.532

Gnomad OTH AF: 0.548

GnomAD4 exome AF: 0.550 AC: 240 AN: 436 Hom.: 59 AF XY: 0.550 AC XY: 144 AN XY: 262

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.547 AC: 233 AN: 426

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.667 AC: 4 AN: 6

Other (OTH) AF: 0.750 AC: 3 AN: 4

GnomAD4 genome AF: 0.528 AC: 80250 AN: 151924 Hom.: 21203 Cov.: 31 AF XY: 0.525 AC XY: 38940 AN XY: 74212

African (AFR) AF: 0.536 AC: 22195 AN: 41434

American (AMR) AF: 0.537 AC: 8213 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.456 AC: 1578 AN: 3464

East Asian (EAS) AF: 0.433 AC: 2230 AN: 5154

South Asian (SAS) AF: 0.563 AC: 2702 AN: 4802

European-Finnish (FIN) AF: 0.528 AC: 5555 AN: 10526

Middle Eastern (MID) AF: 0.466 AC: 135 AN: 290

European-Non Finnish (NFE) AF: 0.532 AC: 36118 AN: 67952

Other (OTH) AF: 0.547 AC: 1158 AN: 2116

Alfa AF: 0.531 Hom.: 36472

Bravo AF: 0.526

Asia WGS AF: 0.478 AC: 1665 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.42
DANN	Benign	0.17
PhyloP100		-0.21

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs947260;

hg19: chr10-124528930;