rs6696438

Variant names:

• chr1-196115362-C-T
• rs6696438
• ENST00000838209.1:n.130+45008G>A

Variant summary

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

The ENST00000838209.1(LINC01724):​n.130+45008G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.116 in 152,154 control chromosomes in the GnomAD database, including 1,130 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 (1130 hom., cov: 32)
• Consequence: LINC01724 ENST00000838209.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.926
• Publications: 4 publications found

Genes affected

LINC01724 (HGNC:52512): (long intergenic non-protein coding RNA 1724)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.227 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000838209.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01724	ENST00000838209.1		n.130+45008G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.116 AC: 17595 AN: 152036 Hom.: 1125 Cov.: 32

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.105

Gnomad ASJ AF: 0.118

Gnomad EAS AF: 0.166

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.169

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.116 AC: 17617 AN: 152154 Hom.: 1130 Cov.: 32 AF XY: 0.120 AC XY: 8897 AN XY: 74368

African (AFR) AF: 0.103 AC: 4289 AN: 41532

American (AMR) AF: 0.105 AC: 1598 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.118 AC: 410 AN: 3468

East Asian (EAS) AF: 0.166 AC: 860 AN: 5170

South Asian (SAS) AF: 0.238 AC: 1146 AN: 4814

European-Finnish (FIN) AF: 0.169 AC: 1786 AN: 10588

Middle Eastern (MID) AF: 0.151 AC: 44 AN: 292

European-Non Finnish (NFE) AF: 0.105 AC: 7141 AN: 67994

Other (OTH) AF: 0.117 AC: 248 AN: 2116

Alfa AF: 0.114 Hom.: 547

Bravo AF: 0.108

Asia WGS AF: 0.228 AC: 790 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.8
DANN	Benign	0.45
PhyloP100		0.93

Splicing

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

Other links and lift over

dbSNP: rs6696438; hg19: chr1-196084492;