rs7071717

Variant names:

• chr10-90058530-A-G
• rs7071717
• ENST00000664430.1:n.549-41762A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000664430.1(LINC01374):​n.549-41762A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0609 in 152,272 control chromosomes in the GnomAD database, including 446 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 0.061 (446 hom., cov: 33)
• Consequence: LINC01374 ENST00000664430.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.312

Genes affected

LINC01374 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.122 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
LINC01374	ENST00000664430.1	n.549-41762A>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.0608 AC: 9254 AN: 152154 Hom.: 442 Cov.: 33

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.0844

Gnomad AMR AF: 0.0364

Gnomad ASJ AF: 0.0164

Gnomad EAS AF: 0.00250

Gnomad SAS AF: 0.0265

Gnomad FIN AF: 0.0127

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0443

Gnomad OTH AF: 0.0507

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

GnomAD4 genome AF: 0.0609 AC: 9267 AN: 152272 Hom.: 446 Cov.: 33 AF XY: 0.0579 AC XY: 4314 AN XY: 74470

Gnomad4 AFR AF: 0.125

Gnomad4 AMR AF: 0.0364

Gnomad4 ASJ AF: 0.0164

Gnomad4 EAS AF: 0.00270

Gnomad4 SAS AF: 0.0270

Gnomad4 FIN AF: 0.0127

Gnomad4 NFE AF: 0.0443

Gnomad4 OTH AF: 0.0497

Alfa AF: 0.0504 Hom.: 37

Bravo AF: 0.0650

Asia WGS AF: 0.0290 AC: 103 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.88
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7071717; hg19: chr10-91818287;