XM_047426130.1:c.1432T>C

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

Genes affected

LOC124900290 (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=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.284 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000442370.6. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000293396	ENST00000442370.6	TSL:2	n.1012T>C		non_coding_transcript_exon	Exon 5 of 5
	DMBT1L1	ENST00000636837.3	TSL:6	n.5693T>C		non_coding_transcript_exon	Exon 24 of 24
	ENSG00000293396	ENST00000728123.1		n.758T>C		non_coding_transcript_exon	Exon 5 of 5

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

African (AFR) AF: 0.153 AC: 2421 AN: 15786

American (AMR) AF: 0.247 AC: 243 AN: 982

Ashkenazi Jewish (ASJ) AF: 0.232 AC: 1196 AN: 5152

East Asian (EAS) AF: 0.302 AC: 1097 AN: 3630

South Asian (SAS) AF: 0.153 AC: 2518 AN: 16460

European-Finnish (FIN) AF: 0.259 AC: 186 AN: 718

Middle Eastern (MID) AF: 0.160 AC: 259 AN: 1620

European-Non Finnish (NFE) AF: 0.229 AC: 174107 AN: 761936

Other (OTH) AF: 0.226 AC: 6178 AN: 27328

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

African (AFR) AF: 0.155 AC: 6443 AN: 41536

American (AMR) AF: 0.263 AC: 4019 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.229 AC: 794 AN: 3470

East Asian (EAS) AF: 0.296 AC: 1529 AN: 5162

South Asian (SAS) AF: 0.148 AC: 714 AN: 4822

European-Finnish (FIN) AF: 0.272 AC: 2879 AN: 10580

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.227 AC: 15439 AN: 67994

Other (OTH) AF: 0.217 AC: 458 AN: 2110

Alfa AF: 0.205 Hom.: 2751

Bravo AF: 0.213

Asia WGS AF: 0.226 AC: 783 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	13
DANN	Benign	0.68
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs11248317; hg19: chr10-124585833;