5-7368732-C-T

Variant names:

• chr5-7368732-C-T
• rs13172324
• ENST00000513219.2:n.275+701G>A

Variant summary

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

The ENST00000513219.2(ENSG00000249865):​n.275+701G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0918 in 152,154 control chromosomes in the GnomAD database, including 719 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 0.092 (719 hom., cov: 32)
• Consequence: ENSG00000249865 ENST00000513219.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.247
• Publications: 5 publications found

Genes affected

ENSG00000249865 (HGNC:):

LINC02142 (HGNC:53002): (long intergenic non-protein coding RNA 2142)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.114 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000513219.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC105374645	NR_188254.1		n.301+701G>A		intron	N/A
	LOC105374645	NR_188255.1		n.356+701G>A		intron	N/A
	LOC105374645	NR_188256.1		n.342+701G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000249865	ENST00000513219.2	TSL:3	n.275+701G>A		intron	N/A
	LINC02142	ENST00000715908.1		n.457+5191C>T		intron	N/A
	ENSG00000249865	ENST00000813050.1		n.313+701G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0918 AC: 13962 AN: 152034 Hom.: 718 Cov.: 32

Gnomad AFR AF: 0.0848

Gnomad AMI AF: 0.0626

Gnomad AMR AF: 0.0647

Gnomad ASJ AF: 0.118

Gnomad EAS AF: 0.0175

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.128

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0991

Gnomad OTH AF: 0.0927

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

GnomAD4 genome AF: 0.0918 AC: 13969 AN: 152154 Hom.: 719 Cov.: 32 AF XY: 0.0920 AC XY: 6843 AN XY: 74380

African (AFR) AF: 0.0848 AC: 3520 AN: 41496

American (AMR) AF: 0.0645 AC: 985 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.118 AC: 409 AN: 3464

East Asian (EAS) AF: 0.0180 AC: 93 AN: 5178

South Asian (SAS) AF: 0.122 AC: 589 AN: 4824

European-Finnish (FIN) AF: 0.128 AC: 1351 AN: 10586

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.0992 AC: 6744 AN: 68008

Other (OTH) AF: 0.0908 AC: 192 AN: 2114

Alfa AF: 0.0903 Hom.: 1069

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	10
DANN	Benign	0.82
PhyloP100		0.25
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs13172324; hg19: chr5-7368845;