10-122826317-T-C

Variant names:

• chr10-122826317-T-C
• rs11248317
• XM_047426130.1:c.1432T>C

Variant summary

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

The XM_047426130.1(LOC124900290):​c.1432T>C​(p.Trp478Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.224 in 985,776 control chromosomes in the GnomAD database, including 25,199 homozygotes. In-silico tool predicts a benign outcome for this variant. 4/4 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.21 (3617 hom., cov: 32)
  • Exomes 𝑓: 0.23 (21582 hom.)
• Consequence: LOC124900290 XM_047426130.1 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.14

Genes affected

LOC124900290 (HGNC:):

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=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.284 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124900290	XM_047426130.1	c.1432T>C	p.Trp478Arg	missense_variant	Exon 8 of 8		XP_047282086.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DMBT1L1	ENST00000442370.6	n.1012T>C		non_coding_transcript_exon_variant	Exon 5 of 5	2
DMBT1L1	ENST00000636837.3	n.5693T>C		non_coding_transcript_exon_variant	Exon 24 of 24	6

Frequencies

GnomAD3 genomes AF: 0.214 AC: 32540 AN: 152044 Hom.: 3613 Cov.: 32

Gnomad AFR AF: 0.155

Gnomad AMI AF: 0.263

Gnomad AMR AF: 0.263

Gnomad ASJ AF: 0.229

Gnomad EAS AF: 0.295

Gnomad SAS AF: 0.148

Gnomad FIN AF: 0.272

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.227

Gnomad OTH AF: 0.218

GnomAD4 exome AF: 0.226 AC: 188205 AN: 833612 Hom.: 21582 Cov.: 30 AF XY: 0.225 AC XY: 86742 AN XY: 385040

Gnomad4 AFR exome AF: 0.153

Gnomad4 AMR exome AF: 0.247

Gnomad4 ASJ exome AF: 0.232

Gnomad4 EAS exome AF: 0.302

Gnomad4 SAS exome AF: 0.153

Gnomad4 FIN exome AF: 0.259

Gnomad4 NFE exome AF: 0.229

Gnomad4 OTH exome AF: 0.226

GnomAD4 genome AF: 0.214 AC: 32564 AN: 152164 Hom.: 3617 Cov.: 32 AF XY: 0.216 AC XY: 16034 AN XY: 74390

Gnomad4 AFR AF: 0.155

Gnomad4 AMR AF: 0.263

Gnomad4 ASJ AF: 0.229

Gnomad4 EAS AF: 0.296

Gnomad4 SAS AF: 0.148

Gnomad4 FIN AF: 0.272

Gnomad4 NFE AF: 0.227

Gnomad4 OTH AF: 0.217

Alfa AF: 0.194 Hom.: 1381

Bravo AF: 0.213

Asia WGS AF: 0.226 AC: 783 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	13
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11248317; hg19: chr10-124585833;