rs271158

Variant names:

• chr6-132955230-A-G
• rs271158
• ENST00000659399.1:n.122+713A>G

Variant summary

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

The ENST00000659399.1(LINC00326):​n.122+713A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.595 in 152,028 control chromosomes in the GnomAD database, including 28,762 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 0.60 (28762 hom., cov: 32)
• Consequence: LINC00326 ENST00000659399.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0790
• Publications: 3 publications found

Genes affected

LINC00326 (HGNC:41926): (long intergenic non-protein coding RNA 326)

LOC105378008 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.826 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378008	XR_001744346.1	n.1059-2887A>G		intron_variant	Intron 7 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00326	ENST00000659399.1	n.122+713A>G		intron_variant	Intron 1 of 2
LINC00326	ENST00000668229.2	n.71+713A>G		intron_variant	Intron 1 of 2
LINC00326	ENST00000669115.3	n.284+630A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.595 AC: 90399 AN: 151910 Hom.: 28715 Cov.: 32

Gnomad AFR AF: 0.795

Gnomad AMI AF: 0.376

Gnomad AMR AF: 0.662

Gnomad ASJ AF: 0.537

Gnomad EAS AF: 0.848

Gnomad SAS AF: 0.650

Gnomad FIN AF: 0.445

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.465

Gnomad OTH AF: 0.602

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

GnomAD4 genome AF: 0.595 AC: 90500 AN: 152028 Hom.: 28762 Cov.: 32 AF XY: 0.597 AC XY: 44318 AN XY: 74296

African (AFR) AF: 0.795 AC: 33003 AN: 41500

American (AMR) AF: 0.662 AC: 10102 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.537 AC: 1865 AN: 3470

East Asian (EAS) AF: 0.847 AC: 4376 AN: 5164

South Asian (SAS) AF: 0.651 AC: 3136 AN: 4820

European-Finnish (FIN) AF: 0.445 AC: 4692 AN: 10554

Middle Eastern (MID) AF: 0.514 AC: 151 AN: 294

European-Non Finnish (NFE) AF: 0.465 AC: 31564 AN: 67946

Other (OTH) AF: 0.602 AC: 1268 AN: 2106

Alfa AF: 0.541 Hom.: 12819

Bravo AF: 0.625

Asia WGS AF: 0.733 AC: 2550 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	6.9
DANN	Benign	0.69
PhyloP100		-0.079

Splicing

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

Other links and lift over

dbSNP: rs271158; hg19: chr6-133276369;