5-67472725-C-T

Position:

• chr5-67472725-C-T

Variant summary

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

The ENST00000508512.5(ENSG00000250978):​n.63+2690G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.895 in 151,964 control chromosomes in the GnomAD database, including 60,935 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 0.90 (60935 hom., cov: 29)
• Consequence: ENSG00000250978 ENST00000508512.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.934

Genes affected

LINC02997 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC101928819	XR_241808.5	n.63+2690G>A		intron_variant
LOC101928819	XR_948390.3	n.85-4672G>A		intron_variant
LOC101928819	XR_948391.3	n.183-4672G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02997	ENST00000503106.5	n.251+93097C>T		intron_variant		4
ENSG00000250978	ENST00000508512.5	n.63+2690G>A		intron_variant		3
ENSG00000250978	ENST00000515184.1	n.178+2690G>A		intron_variant		3
LINC02997	ENST00000668508.1	n.123+14982C>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.895 AC: 135907 AN: 151846 Hom.: 60878 Cov.: 29

Gnomad AFR AF: 0.909

Gnomad AMI AF: 0.813

Gnomad AMR AF: 0.922

Gnomad ASJ AF: 0.900

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.928

Gnomad FIN AF: 0.910

Gnomad MID AF: 0.908

Gnomad NFE AF: 0.869

Gnomad OTH AF: 0.898

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

GnomAD4 genome AF: 0.895 AC: 136021 AN: 151964 Hom.: 60935 Cov.: 29 AF XY: 0.899 AC XY: 66784 AN XY: 74262

Gnomad4 AFR AF: 0.909

Gnomad4 AMR AF: 0.922

Gnomad4 ASJ AF: 0.900

Gnomad4 EAS AF: 0.998

Gnomad4 SAS AF: 0.928

Gnomad4 FIN AF: 0.910

Gnomad4 NFE AF: 0.869

Gnomad4 OTH AF: 0.900

Alfa AF: 0.877 Hom.: 72847

Bravo AF: 0.898

Asia WGS AF: 0.961 AC: 3339 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.31
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1387630; hg19: chr5-66768553;