rs1323565

Positions:

• chr13-75872346-A-G

Variant summary

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

The NR_164111.1(LMO7DN):​n.206+1103A>G variant causes a intron, non coding transcript 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 NR_164111.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.93

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LMO7DN	NR_164111.1	n.206+1103A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LMO7DN	ENST00000318245.5	n.206+1103A>G		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR AF: 0.530

Gnomad4 AMR AF: 0.621

Gnomad4 ASJ AF: 0.732

Gnomad4 EAS AF: 0.304

Gnomad4 SAS AF: 0.624

Gnomad4 FIN AF: 0.647

Gnomad4 NFE AF: 0.655

Gnomad4 OTH AF: 0.632

Alfa AF: 0.635 Hom.: 9685

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

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: rs1323565; hg19: chr13-76446482;