chr3-95121599-C-T

Variant names:

• chr3-95121599-C-T
• rs3849439
• ENST00000462219.6:n.738-16587C>T

Variant summary

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

The ENST00000462219.6(LINC00879):​n.738-16587C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.168 in 152,150 control chromosomes in the GnomAD database, including 2,485 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 0.17 (2485 hom., cov: 32)
• Consequence: LINC00879 ENST00000462219.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.327
• Publications: 5 publications found

Genes affected

LINC00879 (HGNC:48566): (long intergenic non-protein coding RNA 879)

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 (SAS) allele frequency at 95% confidence interval = 0.349 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000462219.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00879	ENST00000462219.6	TSL:2	n.738-16587C>T		intron	N/A
	LINC00879	ENST00000470465.1	TSL:2	n.188-16627C>T		intron	N/A
	LINC00879	ENST00000651942.1		n.609-16587C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.168 AC: 25570 AN: 152032 Hom.: 2477 Cov.: 32

Gnomad AFR AF: 0.197

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.323

Gnomad SAS AF: 0.364

Gnomad FIN AF: 0.175

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.163

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

GnomAD4 genome AF: 0.168 AC: 25591 AN: 152150 Hom.: 2485 Cov.: 32 AF XY: 0.173 AC XY: 12830 AN XY: 74374

African (AFR) AF: 0.197 AC: 8185 AN: 41502

American (AMR) AF: 0.112 AC: 1720 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.129 AC: 448 AN: 3468

East Asian (EAS) AF: 0.322 AC: 1664 AN: 5168

South Asian (SAS) AF: 0.363 AC: 1749 AN: 4818

European-Finnish (FIN) AF: 0.175 AC: 1852 AN: 10582

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.139 AC: 9456 AN: 68000

Other (OTH) AF: 0.168 AC: 356 AN: 2114

Alfa AF: 0.144 Hom.: 2062

Bravo AF: 0.162

Asia WGS AF: 0.360 AC: 1250 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	4.6
DANN	Benign	0.50
PhyloP100		0.33

Splicing

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

Other links and lift over

dbSNP: rs3849439; hg19: chr3-94840443;