rs7618373

Variant names:

• chr3-176619231-G-A
• rs7618373
• ENST00000434969.2:n.788-14545C>T

Variant summary

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

The ENST00000434969.2(LINC01208):​n.788-14545C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.437 in 151,766 control chromosomes in the GnomAD database, including 15,220 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 0.44 (15220 hom., cov: 31)
• Consequence: LINC01208 ENST00000434969.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.492
• Publications: 2 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.569 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000434969.2. 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
	LINC01208	NR_109968.1		n.284-14545C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01208	ENST00000434969.2	TSL:2	n.788-14545C>T		intron	N/A
	LINC01208	ENST00000652470.1		n.280+24825C>T		intron	N/A
	LINC01208	ENST00000657476.1		n.893+7026C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.436 AC: 66188 AN: 151646 Hom.: 15195 Cov.: 31

Gnomad AFR AF: 0.575

Gnomad AMI AF: 0.590

Gnomad AMR AF: 0.442

Gnomad ASJ AF: 0.379

Gnomad EAS AF: 0.477

Gnomad SAS AF: 0.434

Gnomad FIN AF: 0.331

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.367

Gnomad OTH AF: 0.393

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

GnomAD4 genome AF: 0.437 AC: 66273 AN: 151766 Hom.: 15220 Cov.: 31 AF XY: 0.434 AC XY: 32209 AN XY: 74138

African (AFR) AF: 0.575 AC: 23794 AN: 41390

American (AMR) AF: 0.443 AC: 6745 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.379 AC: 1312 AN: 3464

East Asian (EAS) AF: 0.477 AC: 2458 AN: 5158

South Asian (SAS) AF: 0.432 AC: 2074 AN: 4806

European-Finnish (FIN) AF: 0.331 AC: 3479 AN: 10518

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.367 AC: 24935 AN: 67878

Other (OTH) AF: 0.397 AC: 837 AN: 2110

Alfa AF: 0.415 Hom.: 2471

Bravo AF: 0.451

Asia WGS AF: 0.467 AC: 1617 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.2
DANN	Benign	0.43
PhyloP100		-0.49

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: rs7618373;

hg19: chr3-176337019;