rs2169445

Variant names:

• chr13-50757624-G-A
• rs2169445
• ENST00000400393.3:c.460-44384C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

Genes affected

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

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
DLEU7	NM_198989.3	c.460-44384C>T		intron_variant	Intron 1 of 1		NP_945340.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DLEU7	ENST00000400393.3	c.460-44384C>T		intron_variant	Intron 1 of 1	1		ENSP00000420976.1
DLEU1	ENST00000650996.1	n.240-139G>A		intron_variant	Intron 1 of 3
DLEU7	ENST00000651265.1	n.*469-61046C>T		intron_variant	Intron 3 of 3			ENSP00000516017.1

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

African (AFR) AF: 0.0896 AC: 3722 AN: 41524

American (AMR) AF: 0.0145 AC: 221 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.000288 AC: 1 AN: 3468

East Asian (EAS) AF: 0.0585 AC: 303 AN: 5182

South Asian (SAS) AF: 0.0247 AC: 119 AN: 4824

European-Finnish (FIN) AF: 0.0110 AC: 117 AN: 10602

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.00748 AC: 509 AN: 68012

Other (OTH) AF: 0.0208 AC: 44 AN: 2112

Alfa AF: 0.0150 Hom.: 79

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
PhyloP100		1.1
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2169445; hg19: chr13-51331760;