rs7916586

chr10-123402677-G-A

Variant summary

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

The ENST00000662754.1(LINC02641):n.337+41127G>A 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 0.5 in 152,014 control chromosomes in the GnomAD database, including 21,284 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 0.50 (21284 hom., cov: 32)
• Consequence: LINC02641 ENST00000662754.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0370

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.757 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02641	XR_007062326.1	n.8909+40530G>A		intron_variant, non_coding_transcript_variant
LINC02641	XR_002957104.1	n.6362+40530G>A		intron_variant, non_coding_transcript_variant
LINC02641	XR_002957105.1	n.5693+40530G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02641	ENST00000662754.1	n.337+41127G>A		intron_variant, non_coding_transcript_variant
LINC02641	ENST00000448347.5	n.586+40530G>A		intron_variant, non_coding_transcript_variant		3
LINC02641	ENST00000448671.2	n.538+41127G>A		intron_variant, non_coding_transcript_variant		3
LINC02641	ENST00000671662.1	n.824+40530G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.500 AC: 75981 AN: 151894 Hom.: 21251 Cov.: 32

Gnomad AFR AF: 0.764

Gnomad AMI AF: 0.212

Gnomad AMR AF: 0.485

Gnomad ASJ AF: 0.455

Gnomad EAS AF: 0.599

Gnomad SAS AF: 0.339

Gnomad FIN AF: 0.331

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.381

Gnomad OTH AF: 0.480

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

GnomAD4 genome AF: 0.500 AC: 76073 AN: 152014 Hom.: 21284 Cov.: 32 AF XY: 0.496 AC XY: 36859 AN XY: 74316

Gnomad4 AFR AF: 0.764

Gnomad4 AMR AF: 0.485

Gnomad4 ASJ AF: 0.455

Gnomad4 EAS AF: 0.599

Gnomad4 SAS AF: 0.339

Gnomad4 FIN AF: 0.331

Gnomad4 NFE AF: 0.381

Gnomad4 OTH AF: 0.477

Alfa AF: 0.401 Hom.: 25220

Bravo AF: 0.529

Asia WGS AF: 0.455 AC: 1579 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.9
Dann	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7916586; hg19: chr10-125162193;