rs1727638

chr6-71429869-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_121615.1(LINC01626):n.76-70G>A variant causes a intron, non coding transcript 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 NR_121615.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.15

Genes affected

LINC01626 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01626	NR_121615.1	n.76-70G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.678

Gnomad4 AMR AF: 0.528

Gnomad4 ASJ AF: 0.497

Gnomad4 EAS AF: 0.590

Gnomad4 SAS AF: 0.352

Gnomad4 FIN AF: 0.370

Gnomad4 NFE AF: 0.440

Gnomad4 OTH AF: 0.544

Alfa AF: 0.458 Hom.: 25819

Bravo AF: 0.537

Asia WGS AF: 0.501 AC: 1740 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
Cadd	Benign	16
Dann	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1727638; hg19: chr6-72139572;