rs1883628

chr6-1058079-C-T

Variant summary

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

The NR_027116.2(LINC01622):n.1620+41634G>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 0.062 in 152,288 control chromosomes in the GnomAD database, including 403 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 0.062 (403 hom., cov: 33)
• Consequence: LINC01622 NR_027116.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.653

Genes affected

LINC01622 (HGNC:27768): (long intergenic non-protein coding RNA 1622)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0943 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01622	NR_027116.2	n.1620+41634G>A		intron_variant, non_coding_transcript_variant
LINC01622	NR_027115.3	n.1620+41634G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01622	ENST00000655659.1	n.1660+41634G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0621 AC: 9450 AN: 152170 Hom.: 404 Cov.: 33

Gnomad AFR AF: 0.0167

Gnomad AMI AF: 0.110

Gnomad AMR AF: 0.0493

Gnomad ASJ AF: 0.0556

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.0647

Gnomad FIN AF: 0.0654

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0963

Gnomad OTH AF: 0.0675

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

GnomAD4 genome AF: 0.0620 AC: 9448 AN: 152288 Hom.: 403 Cov.: 33 AF XY: 0.0598 AC XY: 4451 AN XY: 74468

Gnomad4 AFR AF: 0.0166

Gnomad4 AMR AF: 0.0492

Gnomad4 ASJ AF: 0.0556

Gnomad4 EAS AF: 0.000772

Gnomad4 SAS AF: 0.0654

Gnomad4 FIN AF: 0.0654

Gnomad4 NFE AF: 0.0962

Gnomad4 OTH AF: 0.0668

Alfa AF: 0.0863 Hom.: 314

Bravo AF: 0.0581

Asia WGS AF: 0.0290 AC: 102 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.43
Dann	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1883628; hg19: chr6-1058314;