rs11255149

Variant names:

• chr10-7469641-T-C
• rs11255149
• ENST00000420395.1:n.33-48A>G

Variant summary

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

The ENST00000420395.1(LINC02642):​n.33-48A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0528 in 152,274 control chromosomes in the GnomAD database, including 308 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 0.053 (308 hom., cov: 32)
  • Exomes 𝑓: 0.17 (0 hom.)
• Consequence: LINC02642 ENST00000420395.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0710
• Publications: 0 publications found

Genes affected

LINC02642 (HGNC:54124): (long intergenic non-protein coding RNA 2642)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.079 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000420395.1. 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
	LINC02642	NR_184107.1		n.81-48A>G		intron	N/A
	LINC02642	NR_184108.1		n.81-48A>G		intron	N/A
	LINC02642	NR_184109.1		n.81-48A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02642	ENST00000420395.1	TSL:3	n.33-48A>G		intron	N/A
	LINC02642	ENST00000660269.1		n.111-48A>G		intron	N/A
	LINC02642	ENST00000670632.2		n.186+45A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0528 AC: 8040 AN: 152150 Hom.: 307 Cov.: 32

Gnomad AFR AF: 0.0145

Gnomad AMI AF: 0.161

Gnomad AMR AF: 0.0582

Gnomad ASJ AF: 0.0865

Gnomad EAS AF: 0.00192

Gnomad SAS AF: 0.0851

Gnomad FIN AF: 0.0294

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.0762

Gnomad OTH AF: 0.0722

GnomAD4 exome AF: 0.167 AC: 1 AN: 6 Hom.: 0 Cov.: 0 AF XY: 0.167 AC XY: 1 AN XY: 6

African (AFR) AF: 0.00 AC: 0 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.250 AC: 1 AN: 4

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.0528 AC: 8038 AN: 152268 Hom.: 308 Cov.: 32 AF XY: 0.0521 AC XY: 3883 AN XY: 74472

African (AFR) AF: 0.0144 AC: 599 AN: 41560

American (AMR) AF: 0.0581 AC: 888 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0865 AC: 300 AN: 3470

East Asian (EAS) AF: 0.00193 AC: 10 AN: 5184

South Asian (SAS) AF: 0.0858 AC: 414 AN: 4826

European-Finnish (FIN) AF: 0.0294 AC: 312 AN: 10622

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.0762 AC: 5182 AN: 68000

Other (OTH) AF: 0.0715 AC: 151 AN: 2112

Alfa AF: 0.0719 Hom.: 801

Bravo AF: 0.0528

Asia WGS AF: 0.0300 AC: 104 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.5
DANN	Benign	0.76
PhyloP100		0.071

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: rs11255149;

hg19: chr10-7511603;