rs7628387

Positions:

• chr3-176845774-A-C

Variant summary

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

The ENST00000428516.1(LINC01208):​n.198+7935T>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 0.198 in 152,104 control chromosomes in the GnomAD database, including 3,550 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 0.20 (3550 hom., cov: 33)
• Consequence: LINC01208 ENST00000428516.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.178

Genes affected

LINC01208 (HGNC:49639): (long intergenic non-protein coding RNA 1208)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.319 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01208	ENST00000428516.1	n.198+7935T>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.198 AC: 30107 AN: 151986 Hom.: 3542 Cov.: 33

Gnomad AFR AF: 0.324

Gnomad AMI AF: 0.193

Gnomad AMR AF: 0.136

Gnomad ASJ AF: 0.0810

Gnomad EAS AF: 0.103

Gnomad SAS AF: 0.168

Gnomad FIN AF: 0.252

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.144

Gnomad OTH AF: 0.160

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

GnomAD4 genome AF: 0.198 AC: 30143 AN: 152104 Hom.: 3550 Cov.: 33 AF XY: 0.200 AC XY: 14885 AN XY: 74356

Gnomad4 AFR AF: 0.324

Gnomad4 AMR AF: 0.135

Gnomad4 ASJ AF: 0.0810

Gnomad4 EAS AF: 0.102

Gnomad4 SAS AF: 0.166

Gnomad4 FIN AF: 0.252

Gnomad4 NFE AF: 0.144

Gnomad4 OTH AF: 0.162

Alfa AF: 0.143 Hom.: 3404

Bravo AF: 0.193

Asia WGS AF: 0.131 AC: 458 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.48
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7628387; hg19: chr3-176563562;