chr13-75872346-A-G

Variant names:

• chr13-75872346-A-G
• rs1323565
• ENST00000318245.5:n.206+1103A>G

Variant summary

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

The ENST00000318245.5(LMO7DN):​n.206+1103A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.606 in 152,120 control chromosomes in the GnomAD database, including 28,544 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 (28544 hom., cov: 33)
• Consequence: LMO7DN ENST00000318245.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.93
• Publications: 2 publications found

Genes affected

LMO7DN (HGNC:44370): (LMO7 downstream neighbor)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.65 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LMO7DN	NR_164111.1	n.206+1103A>G		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LMO7DN	ENST00000318245.5	n.206+1103A>G		intron_variant	Intron 1 of 3	2
LMO7DN	ENST00000715719.1	n.317+1103A>G		intron_variant	Intron 2 of 10
LMO7DN	ENST00000799117.1	n.479+1103A>G		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.606 AC: 92171 AN: 152002 Hom.: 28521 Cov.: 33

Gnomad AFR AF: 0.529

Gnomad AMI AF: 0.805

Gnomad AMR AF: 0.622

Gnomad ASJ AF: 0.732

Gnomad EAS AF: 0.303

Gnomad SAS AF: 0.624

Gnomad FIN AF: 0.647

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.655

Gnomad OTH AF: 0.630

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

GnomAD4 genome AF: 0.606 AC: 92241 AN: 152120 Hom.: 28544 Cov.: 33 AF XY: 0.603 AC XY: 44865 AN XY: 74362

African (AFR) AF: 0.530 AC: 21957 AN: 41466

American (AMR) AF: 0.621 AC: 9496 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.732 AC: 2540 AN: 3470

East Asian (EAS) AF: 0.304 AC: 1575 AN: 5180

South Asian (SAS) AF: 0.624 AC: 3005 AN: 4816

European-Finnish (FIN) AF: 0.647 AC: 6856 AN: 10594

Middle Eastern (MID) AF: 0.670 AC: 197 AN: 294

European-Non Finnish (NFE) AF: 0.655 AC: 44547 AN: 67988

Other (OTH) AF: 0.632 AC: 1334 AN: 2112

Alfa AF: 0.638 Hom.: 12147

Bravo AF: 0.600

Asia WGS AF: 0.498 AC: 1733 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.13
DANN	Benign	0.28
PhyloP100		-2.9
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: rs1323565; hg19: chr13-76446482;