rs7897598

chr10-123501407-A-Cchr10-123501407-A-G

Variant summary

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

The ENST00000662754.1(LINC02641):n.338-22445A>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 0.367 in 151,756 control chromosomes in the GnomAD database, including 10,502 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 0.37 (10502 hom., cov: 31)
• Consequence: LINC02641 ENST00000662754.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -6.63

Genes affected

LINC02641 (HGNC:54125): (long intergenic non-protein coding RNA 2641)

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 (SAS) allele frequency at 95% confidence interval = 0.563 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02641	XR_007062326.1	n.9157+12397A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02641	ENST00000662754.1	n.338-22445A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.367 AC: 55683 AN: 151638 Hom.: 10501 Cov.: 31

Gnomad AFR AF: 0.313

Gnomad AMI AF: 0.623

Gnomad AMR AF: 0.343

Gnomad ASJ AF: 0.393

Gnomad EAS AF: 0.514

Gnomad SAS AF: 0.582

Gnomad FIN AF: 0.357

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.375

Gnomad OTH AF: 0.390

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

GnomAD4 genome AF: 0.367 AC: 55701 AN: 151756 Hom.: 10502 Cov.: 31 AF XY: 0.373 AC XY: 27667 AN XY: 74122

Gnomad4 AFR AF: 0.313

Gnomad4 AMR AF: 0.343

Gnomad4 ASJ AF: 0.393

Gnomad4 EAS AF: 0.514

Gnomad4 SAS AF: 0.581

Gnomad4 FIN AF: 0.357

Gnomad4 NFE AF: 0.375

Gnomad4 OTH AF: 0.388

Alfa AF: 0.376 Hom.: 15284

Bravo AF: 0.358

Asia WGS AF: 0.489 AC: 1702 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.17
Dann	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7897598; hg19: chr10-125260923;