rs6599619

Variant names:

• chr10-122797013-G-A
• rs6599619
• ENST00000439464.6:n.3467+263G>A

Variant summary

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

The ENST00000439464.6(DMBT1L1):​n.3467+263G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.609 in 152,026 control chromosomes in the GnomAD database, including 28,400 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 (28400 hom., cov: 32)
• Consequence: DMBT1L1 ENST00000439464.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28
• Publications: 2 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=-0.9).
• 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 rank	MANE	Protein	UniProt
DMBT1L1	NR_003570.2	n.3467+263G>A		intron_variant	Intron 27 of 27

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DMBT1L1	ENST00000439464.6	n.3467+263G>A		intron_variant	Intron 27 of 27	2
DMBT1L1	ENST00000605982.2	n.60+263G>A		intron_variant	Intron 1 of 2	3
DMBT1L1	ENST00000636837.3	n.3986+1527G>A		intron_variant	Intron 17 of 23	6

Frequencies

GnomAD3 genomes AF: 0.609 AC: 92584 AN: 151908 Hom.: 28394 Cov.: 32

Gnomad AFR AF: 0.519

Gnomad AMI AF: 0.609

Gnomad AMR AF: 0.623

Gnomad ASJ AF: 0.625

Gnomad EAS AF: 0.553

Gnomad SAS AF: 0.732

Gnomad FIN AF: 0.638

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.652

Gnomad OTH AF: 0.611

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.609 AC: 92627 AN: 152026 Hom.: 28400 Cov.: 32 AF XY: 0.611 AC XY: 45416 AN XY: 74312

African (AFR) AF: 0.518 AC: 21482 AN: 41454

American (AMR) AF: 0.623 AC: 9517 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.625 AC: 2169 AN: 3470

East Asian (EAS) AF: 0.552 AC: 2849 AN: 5158

South Asian (SAS) AF: 0.733 AC: 3522 AN: 4808

European-Finnish (FIN) AF: 0.638 AC: 6740 AN: 10566

Middle Eastern (MID) AF: 0.707 AC: 208 AN: 294

European-Non Finnish (NFE) AF: 0.652 AC: 44291 AN: 67968

Other (OTH) AF: 0.612 AC: 1294 AN: 2114

Alfa AF: 0.633 Hom.: 6301

Bravo AF: 0.601

Asia WGS AF: 0.645 AC: 2248 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.045
DANN	Benign	0.54
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs6599619; hg19: chr10-124556529;