6-2595244-C-T

Variant names:

• chr6-2595244-C-T
• rs1001729
• ENST00000840975.1:n.62-31015G>A

Variant summary

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

The ENST00000840975.1(LINC01600):​n.62-31015G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.272 in 151,964 control chromosomes in the GnomAD database, including 5,793 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 0.27 (5793 hom., cov: 32)
• Consequence: LINC01600 ENST00000840975.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.40
• Publications: 2 publications found

Genes affected

LINC01600 (HGNC:21600): (long intergenic non-protein coding RNA 1600)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.477 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01600	ENST00000840975.1	n.62-31015G>A		intron_variant	Intron 1 of 1
LINC01600	ENST00000840976.1	n.359-31015G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.272 AC: 41264 AN: 151846 Hom.: 5779 Cov.: 32

Gnomad AFR AF: 0.260

Gnomad AMI AF: 0.310

Gnomad AMR AF: 0.265

Gnomad ASJ AF: 0.284

Gnomad EAS AF: 0.492

Gnomad SAS AF: 0.288

Gnomad FIN AF: 0.273

Gnomad MID AF: 0.280

Gnomad NFE AF: 0.261

Gnomad OTH AF: 0.275

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

GnomAD4 genome AF: 0.272 AC: 41306 AN: 151964 Hom.: 5793 Cov.: 32 AF XY: 0.274 AC XY: 20347 AN XY: 74240

African (AFR) AF: 0.259 AC: 10747 AN: 41428

American (AMR) AF: 0.266 AC: 4063 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.284 AC: 985 AN: 3470

East Asian (EAS) AF: 0.493 AC: 2538 AN: 5146

South Asian (SAS) AF: 0.288 AC: 1387 AN: 4820

European-Finnish (FIN) AF: 0.273 AC: 2875 AN: 10542

Middle Eastern (MID) AF: 0.277 AC: 81 AN: 292

European-Non Finnish (NFE) AF: 0.261 AC: 17759 AN: 67960

Other (OTH) AF: 0.279 AC: 589 AN: 2112

Alfa AF: 0.268 Hom.: 23680

Bravo AF: 0.276

Asia WGS AF: 0.408 AC: 1421 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.27
DANN	Benign	0.63
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs1001729; hg19: chr6-2595478;