rs7618373

Positions:

• chr3-176619231-G-A

Variant summary

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

The NR_109968.1(LINC01208):​n.284-14545C>T 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 0.437 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 NR_109968.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.492

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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.569 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01208	NR_109968.1	n.284-14545C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01208	ENST00000652470.1	n.280+24825C>T		intron_variant, non_coding_transcript_variant
LINC01208	ENST00000434969.2	n.788-14545C>T		intron_variant, non_coding_transcript_variant		2
LINC01208	ENST00000657476.1	n.893+7026C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.575

Gnomad4 AMR AF: 0.443

Gnomad4 ASJ AF: 0.379

Gnomad4 EAS AF: 0.477

Gnomad4 SAS AF: 0.432

Gnomad4 FIN AF: 0.331

Gnomad4 NFE AF: 0.367

Gnomad4 OTH AF: 0.397

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7618373; hg19: chr3-176337019;