rs7679738

chr4-149201644-T-C

Variant summary

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

The NR_125887.1(LINC02355):n.600-719T>C 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 0.647 in 151,786 control chromosomes in the GnomAD database, including 33,877 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 0.65 (33877 hom., cov: 32)
• Consequence: LINC02355 NR_125887.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.726

Genes affected

LINC02355 (HGNC:53277): (long intergenic non-protein coding RNA 2355)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.892 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02355	NR_125887.1	n.600-719T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02355	ENST00000503100.1	n.600-719T>C		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.647 AC: 98111 AN: 151668 Hom.: 33816 Cov.: 32

Gnomad AFR AF: 0.900

Gnomad AMI AF: 0.482

Gnomad AMR AF: 0.661

Gnomad ASJ AF: 0.587

Gnomad EAS AF: 0.665

Gnomad SAS AF: 0.704

Gnomad FIN AF: 0.496

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.514

Gnomad OTH AF: 0.630

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

GnomAD4 genome AF: 0.647 AC: 98230 AN: 151786 Hom.: 33877 Cov.: 32 AF XY: 0.651 AC XY: 48300 AN XY: 74152

Gnomad4 AFR AF: 0.900

Gnomad4 AMR AF: 0.661

Gnomad4 ASJ AF: 0.587

Gnomad4 EAS AF: 0.665

Gnomad4 SAS AF: 0.703

Gnomad4 FIN AF: 0.496

Gnomad4 NFE AF: 0.514

Gnomad4 OTH AF: 0.630

Alfa AF: 0.540 Hom.: 30296

Bravo AF: 0.668

Asia WGS AF: 0.720 AC: 2502 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	4.0
Dann	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7679738; hg19: chr4-150122796;