rs6599619

Positions:

• chr10-122797013-G-A

Variant summary

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

The NR_003570.2(DMBT1L1):​n.3467+263G>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 0.609 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 NR_003570.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28

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=-0.9).
• 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/exons	MANE	Protein	UniProt
DMBT1L1	NR_003570.2	n.3467+263G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DMBT1L1	ENST00000439464.6	n.3467+263G>A		intron_variant, non_coding_transcript_variant		2
DMBT1L1	ENST00000636837.3	n.3986+1527G>A		intron_variant, non_coding_transcript_variant
DMBT1L1	ENST00000605982.2	n.60+263G>A		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.518

Gnomad4 AMR AF: 0.623

Gnomad4 ASJ AF: 0.625

Gnomad4 EAS AF: 0.552

Gnomad4 SAS AF: 0.733

Gnomad4 FIN AF: 0.638

Gnomad4 NFE AF: 0.652

Gnomad4 OTH AF: 0.612

Alfa AF: 0.635 Hom.: 6203

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6599619; hg19: chr10-124556529;