rs7916586

Variant names:

• chr10-123402677-G-A
• rs7916586
• ENST00000448347.5:n.586+40530G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000448347.5(LINC02641):​n.586+40530G>A variant causes a intron 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 ENST00000448347.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0370
• Publications: 5 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000448347.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02641	ENST00000448347.5	TSL:3	n.586+40530G>A		intron	N/A
	LINC02641	ENST00000448671.2	TSL:3	n.538+41127G>A		intron	N/A
	LINC02641	ENST00000662754.1		n.337+41127G>A		intron	N/A

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

African (AFR) AF: 0.764 AC: 31685 AN: 41478

American (AMR) AF: 0.485 AC: 7419 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.455 AC: 1576 AN: 3464

East Asian (EAS) AF: 0.599 AC: 3083 AN: 5150

South Asian (SAS) AF: 0.339 AC: 1628 AN: 4800

European-Finnish (FIN) AF: 0.331 AC: 3495 AN: 10570

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.381 AC: 25883 AN: 67950

Other (OTH) AF: 0.477 AC: 1005 AN: 2108

Alfa AF: 0.422 Hom.: 63657

Bravo AF: 0.529

Asia WGS AF: 0.455 AC: 1579 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.9
DANN	Benign	0.62
PhyloP100		-0.037

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7916586;

hg19: chr10-125162193;