6-24749185-C-T

Variant names:

• chr6-24749185-C-T
• rs17419851
• ENST00000825031.1:n.278G>A

Variant summary

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

The ENST00000825031.1(ENSG00000307310):​n.278G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 152,202 control chromosomes in the GnomAD database, including 956 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 0.10 (954 hom., cov: 32)
  • Exomes 𝑓: 0.14 (2 hom.)
• Consequence: ENSG00000307310 ENST00000825031.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.06
• Publications: 9 publications found

Genes affected

ENSG00000307310 (HGNC:):

LINC02828 (HGNC:54359): (long intergenic non-protein coding RNA 2828)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.135 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000825031.1. 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
	LINC02828	NR_183315.1		n.195+37C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000307310	ENST00000825031.1		n.278G>A		non_coding_transcript_exon	Exon 1 of 2
	LINC02828	ENST00000423504.3	TSL:2	n.489+37C>T		intron	N/A
	LINC02828	ENST00000453179.1	TSL:4	n.198+37C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.103 AC: 15614 AN: 152042 Hom.: 954 Cov.: 32

Gnomad AFR AF: 0.0529

Gnomad AMI AF: 0.215

Gnomad AMR AF: 0.0815

Gnomad ASJ AF: 0.126

Gnomad EAS AF: 0.00655

Gnomad SAS AF: 0.0598

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.138

Gnomad OTH AF: 0.104

GnomAD4 exome AF: 0.143 AC: 6 AN: 42 Hom.: 2 Cov.: 0 AF XY: 0.176 AC XY: 6 AN XY: 34

African (AFR) AF: 0.00 AC: 0 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 1.00 AC: 2 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.118 AC: 4 AN: 34

Other (OTH) AF: 0.00 AC: 0 AN: 2

GnomAD4 genome AF: 0.103 AC: 15618 AN: 152160 Hom.: 954 Cov.: 32 AF XY: 0.102 AC XY: 7570 AN XY: 74400

African (AFR) AF: 0.0530 AC: 2199 AN: 41524

American (AMR) AF: 0.0813 AC: 1243 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.126 AC: 438 AN: 3470

East Asian (EAS) AF: 0.00657 AC: 34 AN: 5176

South Asian (SAS) AF: 0.0600 AC: 289 AN: 4816

European-Finnish (FIN) AF: 0.150 AC: 1591 AN: 10584

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.138 AC: 9365 AN: 67992

Other (OTH) AF: 0.103 AC: 217 AN: 2112

Alfa AF: 0.121 Hom.: 2354

Bravo AF: 0.0987

Asia WGS AF: 0.0350 AC: 122 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.91
DANN	Benign	0.81
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs17419851; hg19: chr6-24749413;