rs317985

Variant names:

• chr5-67441974-C-T
• rs317985
• ENST00000503106.5:n.251+62346C>T

Variant summary

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

The ENST00000503106.5(LINC02997):​n.251+62346C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.206 in 152,106 control chromosomes in the GnomAD database, including 4,098 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 0.21 (4098 hom., cov: 32)
• Consequence: LINC02997 ENST00000503106.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.336
• Publications: 5 publications found

Genes affected

LINC02997 (HGNC:56113): (long intergenic non-protein coding RNA 2997)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.365 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02997	ENST00000503106.5	n.251+62346C>T		intron_variant	Intron 1 of 3	4

Frequencies

GnomAD3 genomes AF: 0.206 AC: 31381 AN: 151988 Hom.: 4099 Cov.: 32

Gnomad AFR AF: 0.0531

Gnomad AMI AF: 0.418

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.209

Gnomad EAS AF: 0.379

Gnomad SAS AF: 0.185

Gnomad FIN AF: 0.209

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.287

Gnomad OTH AF: 0.189

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

GnomAD4 genome AF: 0.206 AC: 31380 AN: 152106 Hom.: 4098 Cov.: 32 AF XY: 0.201 AC XY: 14957 AN XY: 74322

African (AFR) AF: 0.0529 AC: 2196 AN: 41528

American (AMR) AF: 0.200 AC: 3059 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.209 AC: 726 AN: 3472

East Asian (EAS) AF: 0.379 AC: 1955 AN: 5156

South Asian (SAS) AF: 0.186 AC: 899 AN: 4824

European-Finnish (FIN) AF: 0.209 AC: 2205 AN: 10572

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.287 AC: 19516 AN: 67952

Other (OTH) AF: 0.190 AC: 402 AN: 2112

Alfa AF: 0.261 Hom.: 3144

Bravo AF: 0.200

Asia WGS AF: 0.279 AC: 963 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	6.1
DANN	Benign	0.27
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs317985; hg19: chr5-66737802;