chr10-64969588-A-G

Variant names:

• chr10-64969588-A-G
• rs4746479
• ENST00000655566.1:n.214+30537T>C

Variant summary

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

The ENST00000655566.1(LINC02671):​n.214+30537T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.861 in 151,992 control chromosomes in the GnomAD database, including 56,630 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 0.86 (56630 hom., cov: 31)
• Consequence: LINC02671 ENST00000655566.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.161
• Publications: 1 publications found

Genes affected

LINC02671 (HGNC:54158): (long intergenic non-protein coding RNA 2671)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.936 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02671	ENST00000655566.1	n.214+30537T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.861 AC: 130765 AN: 151874 Hom.: 56576 Cov.: 31

Gnomad AFR AF: 0.944

Gnomad AMI AF: 0.800

Gnomad AMR AF: 0.814

Gnomad ASJ AF: 0.791

Gnomad EAS AF: 0.765

Gnomad SAS AF: 0.895

Gnomad FIN AF: 0.862

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.831

Gnomad OTH AF: 0.839

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

GnomAD4 genome AF: 0.861 AC: 130881 AN: 151992 Hom.: 56630 Cov.: 31 AF XY: 0.862 AC XY: 64061 AN XY: 74288

African (AFR) AF: 0.944 AC: 39182 AN: 41494

American (AMR) AF: 0.814 AC: 12397 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.791 AC: 2746 AN: 3470

East Asian (EAS) AF: 0.765 AC: 3921 AN: 5126

South Asian (SAS) AF: 0.895 AC: 4327 AN: 4834

European-Finnish (FIN) AF: 0.862 AC: 9132 AN: 10596

Middle Eastern (MID) AF: 0.844 AC: 248 AN: 294

European-Non Finnish (NFE) AF: 0.831 AC: 56427 AN: 67926

Other (OTH) AF: 0.838 AC: 1771 AN: 2114

Alfa AF: 0.845 Hom.: 7684

Bravo AF: 0.858

Asia WGS AF: 0.834 AC: 2903 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.0
DANN	Benign	0.77
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs4746479; hg19: chr10-66729346;