rs7628387

Variant names:

• chr3-176845774-A-C
• rs7628387
• ENST00000428516.1:n.198+7935T>G

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 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
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01208	ENST00000428516.1	n.198+7935T>G		intron_variant	Intron 2 of 4	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;