rs7916571

Variant names:

• chr10-122792263-T-A
• rs7916571
• ENST00000439464.6:n.2774-24T>A

Your query was ambiguous. Multiple possible variants found:

• chr10-122792263-T-A
• chr10-122792263-T-C

Variant summary

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

The ENST00000439464.6(DMBT1L1):​n.2774-24T>A variant causes a intron 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 ENST00000439464.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.90
• 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=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.712 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.2774-24T>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DMBT1L1	ENST00000439464.6	TSL:2	n.2774-24T>A		intron	N/A
	DMBT1L1	ENST00000636837.3	TSL:6	n.3615-24T>A		intron	N/A

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

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: 0.690 AC: 290 AN: 420

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.500 AC: 1 AN: 2

Other (OTH) AF: 0.667 AC: 4 AN: 6

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

African (AFR) AF: 0.533 AC: 22087 AN: 41428

American (AMR) AF: 0.626 AC: 9564 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.625 AC: 2171 AN: 3472

East Asian (EAS) AF: 0.551 AC: 2833 AN: 5142

South Asian (SAS) AF: 0.732 AC: 3527 AN: 4818

European-Finnish (FIN) AF: 0.638 AC: 6732 AN: 10552

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

European-Non Finnish (NFE) AF: 0.652 AC: 44323 AN: 67976

Other (OTH) AF: 0.617 AC: 1298 AN: 2104

Alfa AF: 0.456 Hom.: 1002

Bravo AF: 0.606

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.025
DANN	Benign	0.48
PhyloP100		-1.9

Splicing

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

Other links and lift over

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