rs10499631

chr7-42687019-A-Gchr7-42687019-A-T

Variant summary

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

The NR_110833.1(LINC01448):n.218-14048T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.297 in 152,078 control chromosomes in the GnomAD database, including 6,864 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 0.30 (6864 hom., cov: 33)
• Consequence: LINC01448 NR_110833.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.762

Genes affected

LINC01448 (HGNC:50790): (long intergenic non-protein coding RNA 1448)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.426 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01448	NR_110833.1	n.218-14048T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01448	ENST00000455947.2	n.218-14048T>C		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.297 AC: 45139 AN: 151960 Hom.: 6862 Cov.: 33

Gnomad AFR AF: 0.255

Gnomad AMI AF: 0.205

Gnomad AMR AF: 0.380

Gnomad ASJ AF: 0.254

Gnomad EAS AF: 0.442

Gnomad SAS AF: 0.325

Gnomad FIN AF: 0.336

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.289

Gnomad OTH AF: 0.286

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

GnomAD4 genome AF: 0.297 AC: 45157 AN: 152078 Hom.: 6864 Cov.: 33 AF XY: 0.303 AC XY: 22505 AN XY: 74322

Gnomad4 AFR AF: 0.254

Gnomad4 AMR AF: 0.380

Gnomad4 ASJ AF: 0.254

Gnomad4 EAS AF: 0.441

Gnomad4 SAS AF: 0.325

Gnomad4 FIN AF: 0.336

Gnomad4 NFE AF: 0.289

Gnomad4 OTH AF: 0.286

Alfa AF: 0.297 Hom.: 1181

Bravo AF: 0.294

Asia WGS AF: 0.361 AC: 1259 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	3.0
Dann	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10499631; hg19: chr7-42726618;