rs9317297

Variant names:

• chr13-63247365-G-A
• rs9317297
• ENST00000439454.3:n.250-15234C>T

Variant summary

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

The ENST00000439454.3(LINC00376):​n.250-15234C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0811 in 152,054 control chromosomes in the GnomAD database, including 681 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 0.081 (681 hom., cov: 32)
• Consequence: LINC00376 ENST00000439454.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.146
• Publications: 1 publications found

Genes affected

LINC00376 (HGNC:42701): (long intergenic non-protein coding RNA 376)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.173 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00376	NR_126409.1	n.215-15234C>T		intron_variant	Intron 3 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00376	ENST00000439454.3	n.250-15234C>T		intron_variant	Intron 3 of 6	5
LINC00376	ENST00000836363.1	n.249+16846C>T		intron_variant	Intron 3 of 5
LINC00376	ENST00000836364.1	n.259+16846C>T		intron_variant	Intron 3 of 5

Frequencies

GnomAD3 genomes AF: 0.0812 AC: 12331 AN: 151934 Hom.: 679 Cov.: 32

Gnomad AFR AF: 0.0186

Gnomad AMI AF: 0.0471

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.0565

Gnomad EAS AF: 0.128

Gnomad SAS AF: 0.0905

Gnomad FIN AF: 0.101

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0920

Gnomad OTH AF: 0.0809

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

GnomAD4 genome AF: 0.0811 AC: 12336 AN: 152054 Hom.: 681 Cov.: 32 AF XY: 0.0839 AC XY: 6235 AN XY: 74310

African (AFR) AF: 0.0186 AC: 772 AN: 41562

American (AMR) AF: 0.179 AC: 2731 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.0565 AC: 196 AN: 3468

East Asian (EAS) AF: 0.128 AC: 658 AN: 5150

South Asian (SAS) AF: 0.0910 AC: 439 AN: 4824

European-Finnish (FIN) AF: 0.101 AC: 1065 AN: 10580

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0920 AC: 6244 AN: 67888

Other (OTH) AF: 0.0786 AC: 166 AN: 2112

Alfa AF: 0.0919 Hom.: 399

Bravo AF: 0.0848

Asia WGS AF: 0.0850 AC: 298 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.1
DANN	Benign	0.29
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs9317297; hg19: chr13-63821498;