rs7628387

Variant names:

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

Variant summary

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

The ENST00000794389.1(LINC01208):​n.186+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 ENST00000794389.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.178
• Publications: 3 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000794389.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01208	ENST00000428516.1	TSL:5	n.198+7935T>G		intron	N/A
	LINC01208	ENST00000794389.1		n.186+7935T>G		intron	N/A

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

African (AFR) AF: 0.324 AC: 13433 AN: 41476

American (AMR) AF: 0.135 AC: 2071 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0810 AC: 281 AN: 3468

East Asian (EAS) AF: 0.102 AC: 529 AN: 5176

South Asian (SAS) AF: 0.166 AC: 804 AN: 4830

European-Finnish (FIN) AF: 0.252 AC: 2664 AN: 10560

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.144 AC: 9820 AN: 67996

Other (OTH) AF: 0.162 AC: 340 AN: 2104

Alfa AF: 0.152 Hom.: 8376

Bravo AF: 0.193

Asia WGS AF: 0.131 AC: 458 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.48
DANN	Benign	0.54
PhyloP100		-0.18

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7628387;

hg19: chr3-176563562;