rs1883628

Variant names:

• chr6-1058079-C-T
• rs1883628
• ENST00000612554.2:n.557+41634G>A

Variant summary

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

The ENST00000612554.2(LINC01622):​n.557+41634G>A variant causes a intron 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 ENST00000612554.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.653
• Publications: 0 publications found

Genes affected

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

ENSG00000297704 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000612554.2. 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
	LINC01622	NR_027115.3		n.1620+41634G>A		intron	N/A
	LINC01622	NR_027116.2		n.1620+41634G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01622	ENST00000612554.2	TSL:3	n.557+41634G>A		intron	N/A
	LINC01622	ENST00000655659.1		n.1660+41634G>A		intron	N/A
	LINC01622	ENST00000662378.1		n.1674+41634G>A		intron	N/A

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

African (AFR) AF: 0.0166 AC: 690 AN: 41560

American (AMR) AF: 0.0492 AC: 753 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0556 AC: 193 AN: 3472

East Asian (EAS) AF: 0.000772 AC: 4 AN: 5184

South Asian (SAS) AF: 0.0654 AC: 315 AN: 4816

European-Finnish (FIN) AF: 0.0654 AC: 694 AN: 10616

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0962 AC: 6546 AN: 68018

Other (OTH) AF: 0.0668 AC: 141 AN: 2112

Alfa AF: 0.0743 Hom.: 416

Bravo AF: 0.0581

Asia WGS AF: 0.0290 AC: 102 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.43
DANN	Benign	0.25
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs1883628; hg19: chr6-1058314;