ENST00000816723.1:n.94+8768G>A

Variant names:

• chr6-71429869-G-A
• rs1727638
• ENST00000816723.1:n.94+8768G>A

Variant summary

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

The ENST00000816723.1(LINC01626):​n.94+8768G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.514 in 151,888 control chromosomes in the GnomAD database, including 20,981 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 0.51 (20981 hom., cov: 31)
• Consequence: LINC01626 ENST00000816723.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.15
• Publications: 9 publications found

Genes affected

LINC01626 (HGNC:52257): (long intergenic non-protein coding RNA 1626)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.671 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000816723.1. 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
	LINC01626	NR_121615.1		n.76-70G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01626	ENST00000816723.1		n.94+8768G>A		intron	N/A
	LINC01626	ENST00000816724.1		n.63-70G>A		intron	N/A
	LINC01626	ENST00000816725.1		n.120-70G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.513 AC: 77926 AN: 151770 Hom.: 20935 Cov.: 31

Gnomad AFR AF: 0.678

Gnomad AMI AF: 0.345

Gnomad AMR AF: 0.528

Gnomad ASJ AF: 0.497

Gnomad EAS AF: 0.590

Gnomad SAS AF: 0.351

Gnomad FIN AF: 0.370

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.440

Gnomad OTH AF: 0.540

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

GnomAD4 genome AF: 0.514 AC: 78036 AN: 151888 Hom.: 20981 Cov.: 31 AF XY: 0.507 AC XY: 37661 AN XY: 74246

African (AFR) AF: 0.678 AC: 28089 AN: 41426

American (AMR) AF: 0.528 AC: 8074 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.497 AC: 1724 AN: 3472

East Asian (EAS) AF: 0.590 AC: 3044 AN: 5158

South Asian (SAS) AF: 0.352 AC: 1697 AN: 4820

European-Finnish (FIN) AF: 0.370 AC: 3888 AN: 10506

Middle Eastern (MID) AF: 0.524 AC: 154 AN: 294

European-Non Finnish (NFE) AF: 0.440 AC: 29905 AN: 67904

Other (OTH) AF: 0.544 AC: 1147 AN: 2108

Alfa AF: 0.468 Hom.: 60300

Bravo AF: 0.537

Asia WGS AF: 0.501 AC: 1740 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	16
DANN	Benign	0.51
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs1727638; hg19: chr6-72139572;