chr10-105822379-T-A

Variant names:

• chr10-105822379-T-A
• rs7922744
• ENST00000836861.1:n.215-942A>T

Variant summary

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

The ENST00000836861.1(LINC02627):​n.215-942A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.131 in 152,186 control chromosomes in the GnomAD database, including 3,677 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 0.13 (3677 hom., cov: 33)
• Consequence: LINC02627 ENST00000836861.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.322
• Publications: 3 publications found

Genes affected

LINC02627 (HGNC:54106): (long intergenic non-protein coding RNA 2627)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.413 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000836861.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02627	ENST00000836861.1		n.215-942A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.131 AC: 19851 AN: 152068 Hom.: 3659 Cov.: 33

Gnomad AFR AF: 0.418

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0463

Gnomad ASJ AF: 0.0127

Gnomad EAS AF: 0.0135

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.00263

Gnomad MID AF: 0.0510

Gnomad NFE AF: 0.0141

Gnomad OTH AF: 0.104

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

GnomAD4 genome AF: 0.131 AC: 19920 AN: 152186 Hom.: 3677 Cov.: 33 AF XY: 0.128 AC XY: 9527 AN XY: 74440

African (AFR) AF: 0.418 AC: 17335 AN: 41436

American (AMR) AF: 0.0461 AC: 705 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0127 AC: 44 AN: 3468

East Asian (EAS) AF: 0.0135 AC: 70 AN: 5192

South Asian (SAS) AF: 0.111 AC: 534 AN: 4824

European-Finnish (FIN) AF: 0.00263 AC: 28 AN: 10628

Middle Eastern (MID) AF: 0.0582 AC: 17 AN: 292

European-Non Finnish (NFE) AF: 0.0141 AC: 961 AN: 68028

Other (OTH) AF: 0.107 AC: 226 AN: 2112

Alfa AF: 0.0119 Hom.: 17

Bravo AF: 0.144

Asia WGS AF: 0.113 AC: 392 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.1
DANN	Benign	0.61
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs7922744; hg19: chr10-107582137;