rs699213

Variant names:

• chr10-90210931-C-G
• rs699213
• ENST00000664430.1:n.696-14108C>G

Your query was ambiguous. Multiple possible variants found:

• chr10-90210931-C-G
• chr10-90210931-C-T

Variant summary

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

The ENST00000664430.1(LINC01374):​n.696-14108C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.323 in 151,906 control chromosomes in the GnomAD database, including 8,750 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 0.32 (8750 hom., cov: 32)
• Consequence: LINC01374 ENST00000664430.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.408

Genes affected

LINC01374 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.468 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.696-14108C>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.323 AC: 48963 AN: 151788 Hom.: 8747 Cov.: 32

Gnomad AFR AF: 0.474

Gnomad AMI AF: 0.311

Gnomad AMR AF: 0.267

Gnomad ASJ AF: 0.206

Gnomad EAS AF: 0.473

Gnomad SAS AF: 0.316

Gnomad FIN AF: 0.270

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.247

Gnomad OTH AF: 0.311

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

GnomAD4 genome AF: 0.323 AC: 48992 AN: 151906 Hom.: 8750 Cov.: 32 AF XY: 0.324 AC XY: 24055 AN XY: 74212

Gnomad4 AFR AF: 0.474

Gnomad4 AMR AF: 0.267

Gnomad4 ASJ AF: 0.206

Gnomad4 EAS AF: 0.474

Gnomad4 SAS AF: 0.316

Gnomad4 FIN AF: 0.270

Gnomad4 NFE AF: 0.247

Gnomad4 OTH AF: 0.308

Alfa AF: 0.289 Hom.: 843

Bravo AF: 0.328

Asia WGS AF: 0.370 AC: 1290 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.2
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs699213; hg19: chr10-91970688;