rs7775514

Variant names:

• chr6-134411097-T-A
• rs7775514
• ENST00000431422.3:n.54-26218T>A

Variant summary

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

The ENST00000431422.3(LINC01010):​n.54-26218T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.348 in 152,204 control chromosomes in the GnomAD database, including 15,141 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 0.35 (15141 hom., cov: 33)
• Consequence: LINC01010 ENST00000431422.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.581
• Publications: 3 publications found

Genes affected

LINC01010 (HGNC:48978): (long intergenic non-protein coding RNA 1010)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.781 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
LINC01010	ENST00000431422.3	n.54-26218T>A		intron_variant	Intron 1 of 3	2
LINC01010	ENST00000660399.1	n.54-53644T>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.348 AC: 52900 AN: 152084 Hom.: 15091 Cov.: 33

Gnomad AFR AF: 0.788

Gnomad AMI AF: 0.334

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.341

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.178

Gnomad FIN AF: 0.104

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.360

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

GnomAD4 genome AF: 0.348 AC: 52992 AN: 152204 Hom.: 15141 Cov.: 33 AF XY: 0.339 AC XY: 25213 AN XY: 74418

African (AFR) AF: 0.788 AC: 32740 AN: 41522

American (AMR) AF: 0.232 AC: 3539 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.341 AC: 1185 AN: 3470

East Asian (EAS) AF: 0.158 AC: 819 AN: 5178

South Asian (SAS) AF: 0.177 AC: 854 AN: 4822

European-Finnish (FIN) AF: 0.104 AC: 1104 AN: 10606

Middle Eastern (MID) AF: 0.422 AC: 124 AN: 294

European-Non Finnish (NFE) AF: 0.170 AC: 11570 AN: 68010

Other (OTH) AF: 0.356 AC: 752 AN: 2114

Alfa AF: 0.270 Hom.: 1219

Bravo AF: 0.378

Asia WGS AF: 0.198 AC: 691 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.8
DANN	Benign	0.67
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs7775514; hg19: chr6-134732235;