rs2169445

Positions:

• chr13-50757624-G-A

Variant summary

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

The ENST00000400393.3(DLEU7):​c.460-44384C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0331 in 152,210 control chromosomes in the GnomAD database, including 172 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 0.033 (172 hom., cov: 32)
• Consequence: DLEU7 ENST00000400393.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.12

Genes affected

DLEU7 (HGNC:17567): (deleted in lymphocytic leukemia 7)

DLEU1 (HGNC:13747): (deleted in lymphocytic leukemia 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0872 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DLEU7	NM_198989.3	c.460-44384C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DLEU7	ENST00000400393.3	c.460-44384C>T		intron_variant		1
DLEU7	ENST00000651265.1	c.*469-61046C>T		intron_variant, NMD_transcript_variant
DLEU7	ENST00000651397.1	c.427-61046C>T		intron_variant, NMD_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0331 AC: 5039 AN: 152092 Hom.: 173 Cov.: 32

Gnomad AFR AF: 0.0897

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0145

Gnomad ASJ AF: 0.000288

Gnomad EAS AF: 0.0591

Gnomad SAS AF: 0.0249

Gnomad FIN AF: 0.0110

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.00748

Gnomad OTH AF: 0.0206

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

GnomAD4 genome AF: 0.0331 AC: 5042 AN: 152210 Hom.: 172 Cov.: 32 AF XY: 0.0327 AC XY: 2435 AN XY: 74406

Gnomad4 AFR AF: 0.0896

Gnomad4 AMR AF: 0.0145

Gnomad4 ASJ AF: 0.000288

Gnomad4 EAS AF: 0.0585

Gnomad4 SAS AF: 0.0247

Gnomad4 FIN AF: 0.0110

Gnomad4 NFE AF: 0.00748

Gnomad4 OTH AF: 0.0208

Alfa AF: 0.0113 Hom.: 36

Bravo AF: 0.0366

Asia WGS AF: 0.0490 AC: 171 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.9
DANN	Benign	0.82

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs2169445; hg19: chr13-51331760;