7-26544101-G-T

Variant names:

• chr7-26544101-G-T
• rs17284017
• ENST00000780721.1:n.1221C>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000780721.1(ENSG00000301666):​n.1221C>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 0.12 in 152,250 control chromosomes in the GnomAD database, including 1,211 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 0.12 (1211 hom., cov: 33)
• Consequence: ENSG00000301666 ENST00000780721.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.62
• Publications: 1 publications found

Genes affected

ENSG00000301666 (HGNC:):

LINC03095 (HGNC:56738): (long intergenic non-protein coding RNA 3095)

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.22).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.176 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000780721.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000301666	ENST00000780721.1		n.1221C>A		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000301666	ENST00000780722.1		n.755C>A		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000301666	ENST00000780723.1		n.976C>A		non_coding_transcript_exon	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.120 AC: 18206 AN: 152132 Hom.: 1208 Cov.: 33

Gnomad AFR AF: 0.0609

Gnomad AMI AF: 0.188

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.142

Gnomad EAS AF: 0.0548

Gnomad SAS AF: 0.187

Gnomad FIN AF: 0.169

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.120 AC: 18215 AN: 152250 Hom.: 1211 Cov.: 33 AF XY: 0.122 AC XY: 9057 AN XY: 74434

African (AFR) AF: 0.0611 AC: 2539 AN: 41572

American (AMR) AF: 0.104 AC: 1586 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.142 AC: 493 AN: 3468

East Asian (EAS) AF: 0.0551 AC: 286 AN: 5186

South Asian (SAS) AF: 0.186 AC: 898 AN: 4816

European-Finnish (FIN) AF: 0.169 AC: 1792 AN: 10586

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.150 AC: 10179 AN: 68004

Other (OTH) AF: 0.110 AC: 233 AN: 2110

Alfa AF: 0.130 Hom.: 1859

Bravo AF: 0.109

Asia WGS AF: 0.106 AC: 369 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.22
CADD	Benign	18
DANN	Benign	0.86
PhyloP100		1.6

Splicing

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

Other links and lift over

dbSNP: rs17284017; hg19: chr7-26583720; COSMIC: COSV53495504;