10-90202913-A-G

Variant names:

• chr10-90202913-A-G
• rs2250245
• ENST00000664430.1:n.696-22126A>G

Variant summary

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

The ENST00000664430.1(LINC01374):​n.696-22126A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.33 in 151,742 control chromosomes in the GnomAD database, including 9,134 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 0.33 (9134 hom., cov: 32)
• Consequence: LINC01374 ENST00000664430.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.876

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 = 0.476 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.696-22126A>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.330 AC: 50032 AN: 151624 Hom.: 9132 Cov.: 32

Gnomad AFR AF: 0.482

Gnomad AMI AF: 0.338

Gnomad AMR AF: 0.274

Gnomad ASJ AF: 0.208

Gnomad EAS AF: 0.472

Gnomad SAS AF: 0.325

Gnomad FIN AF: 0.274

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.255

Gnomad OTH AF: 0.315

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

GnomAD4 genome AF: 0.330 AC: 50061 AN: 151742 Hom.: 9134 Cov.: 32 AF XY: 0.331 AC XY: 24556 AN XY: 74176

Gnomad4 AFR AF: 0.481

Gnomad4 AMR AF: 0.274

Gnomad4 ASJ AF: 0.208

Gnomad4 EAS AF: 0.473

Gnomad4 SAS AF: 0.326

Gnomad4 FIN AF: 0.274

Gnomad4 NFE AF: 0.255

Gnomad4 OTH AF: 0.312

Alfa AF: 0.266 Hom.: 9529

Bravo AF: 0.335

Asia WGS AF: 0.380 AC: 1324 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	3.9
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2250245; hg19: chr10-91962670;