rs7679738

Variant names:

• chr4-149201644-T-C
• rs7679738
• ENST00000503100.1:n.600-719T>C

Variant summary

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

The ENST00000503100.1(LINC02355):​n.600-719T>C variant causes a intron 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 ENST00000503100.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.726
• Publications: 3 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000503100.1. 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
	LINC02355	NR_125887.1		n.600-719T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02355	ENST00000503100.1	TSL:1	n.600-719T>C		intron	N/A

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

African (AFR) AF: 0.900 AC: 37347 AN: 41502

American (AMR) AF: 0.661 AC: 10035 AN: 15186

Ashkenazi Jewish (ASJ) AF: 0.587 AC: 2033 AN: 3464

East Asian (EAS) AF: 0.665 AC: 3403 AN: 5120

South Asian (SAS) AF: 0.703 AC: 3390 AN: 4824

European-Finnish (FIN) AF: 0.496 AC: 5235 AN: 10562

Middle Eastern (MID) AF: 0.592 AC: 174 AN: 294

European-Non Finnish (NFE) AF: 0.514 AC: 34847 AN: 67818

Other (OTH) AF: 0.630 AC: 1327 AN: 2106

Alfa AF: 0.551 Hom.: 40146

Bravo AF: 0.668

Asia WGS AF: 0.720 AC: 2502 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	4.0
DANN	Benign	0.48
PhyloP100		-0.73

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: rs7679738;

hg19: chr4-150122796;