chr3-157229227-G-A

Variant names:

• chr3-157229227-G-A
• rs10513505
• ENST00000460796.2:n.168-10363G>A

Variant summary

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

The ENST00000460796.2(LINC00881):​n.168-10363G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0547 in 152,244 control chromosomes in the GnomAD database, including 660 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 0.055 (660 hom., cov: 32)
• Consequence: LINC00881 ENST00000460796.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.404
• Publications: 1 publications found

Genes affected

LINC00881 (HGNC:48567): (long intergenic non-protein coding RNA 881)

LOC101928236 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.173 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101928236	XR_007096141.1	n.1498-10363G>A		intron_variant	Intron 2 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00881	ENST00000460796.2	n.168-10363G>A		intron_variant	Intron 1 of 1	3
LINC00881	ENST00000487238.5	n.122-10363G>A		intron_variant	Intron 1 of 2	4
LINC00881	ENST00000488040.6	n.181-10363G>A		intron_variant	Intron 1 of 2	4

Frequencies

GnomAD3 genomes AF: 0.0547 AC: 8315 AN: 152126 Hom.: 662 Cov.: 32

Gnomad AFR AF: 0.177

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0226

Gnomad ASJ AF: 0.0176

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00891

Gnomad FIN AF: 0.00132

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.00611

Gnomad OTH AF: 0.0450

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

GnomAD4 genome AF: 0.0547 AC: 8330 AN: 152244 Hom.: 660 Cov.: 32 AF XY: 0.0536 AC XY: 3987 AN XY: 74436

African (AFR) AF: 0.177 AC: 7342 AN: 41516

American (AMR) AF: 0.0225 AC: 345 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0176 AC: 61 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5184

South Asian (SAS) AF: 0.00975 AC: 47 AN: 4822

European-Finnish (FIN) AF: 0.00132 AC: 14 AN: 10612

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.00612 AC: 416 AN: 68022

Other (OTH) AF: 0.0445 AC: 94 AN: 2112

Alfa AF: 0.0172 Hom.: 24

Bravo AF: 0.0602

Asia WGS AF: 0.0100 AC: 36 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	9.1
DANN	Benign	0.67
PhyloP100		0.40

Splicing

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

Other links and lift over

dbSNP: rs10513505; hg19: chr3-156947016;