10-43912449-T-G

Variant names:

• chr10-43912449-T-G
• rs2274241
• ENST00000446107.2:n.60T>G

Variant summary

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

The ENST00000446107.2(LINC00841):​n.60T>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.59 in 152,212 control chromosomes in the GnomAD database, including 26,639 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 0.59 (26586 hom., cov: 31)
  • Exomes 𝑓: 0.64 (53 hom.)
• Consequence: LINC00841 ENST00000446107.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.48
• Publications: 3 publications found

Genes affected

LINC00841 (HGNC:27430): (long intergenic non-protein coding RNA 841)

LINC02659 (HGNC:54145): (long intergenic non-protein coding RNA 2659)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.673 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000446107.2. 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
	LINC00841	NR_136148.1		n.48T>G		non_coding_transcript_exon	Exon 1 of 2
	LINC00841	NR_033846.2		n.191+2790T>G		intron	N/A
	LINC00841	NR_136147.1		n.191+2790T>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00841	ENST00000446107.2	TSL:2	n.60T>G		non_coding_transcript_exon	Exon 1 of 2
	LINC00841	ENST00000826345.1		n.40T>G		non_coding_transcript_exon	Exon 1 of 3
	LINC00841	ENST00000826346.1		n.38T>G		non_coding_transcript_exon	Exon 1 of 5

Frequencies

GnomAD3 genomes AF: 0.590 AC: 89623 AN: 151834 Hom.: 26569 Cov.: 31

Gnomad AFR AF: 0.532

Gnomad AMI AF: 0.573

Gnomad AMR AF: 0.544

Gnomad ASJ AF: 0.645

Gnomad EAS AF: 0.611

Gnomad SAS AF: 0.693

Gnomad FIN AF: 0.683

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.609

Gnomad OTH AF: 0.597

GnomAD4 exome AF: 0.641 AC: 168 AN: 262 Hom.: 53 Cov.: 0 AF XY: 0.644 AC XY: 112 AN XY: 174

African (AFR) AF: 0.500 AC: 3 AN: 6

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.500 AC: 2 AN: 4

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.610 AC: 50 AN: 82

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.665 AC: 105 AN: 158

Other (OTH) AF: 0.667 AC: 8 AN: 12

GnomAD4 genome AF: 0.590 AC: 89667 AN: 151950 Hom.: 26586 Cov.: 31 AF XY: 0.595 AC XY: 44192 AN XY: 74250

African (AFR) AF: 0.532 AC: 22026 AN: 41410

American (AMR) AF: 0.543 AC: 8300 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.645 AC: 2240 AN: 3472

East Asian (EAS) AF: 0.612 AC: 3148 AN: 5148

South Asian (SAS) AF: 0.692 AC: 3334 AN: 4816

European-Finnish (FIN) AF: 0.683 AC: 7222 AN: 10570

Middle Eastern (MID) AF: 0.694 AC: 204 AN: 294

European-Non Finnish (NFE) AF: 0.609 AC: 41403 AN: 67946

Other (OTH) AF: 0.601 AC: 1267 AN: 2108

Alfa AF: 0.596 Hom.: 3373

Bravo AF: 0.569

Asia WGS AF: 0.651 AC: 2264 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.28
DANN	Benign	0.47
PhyloP100		-2.5

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: rs2274241;

hg19: chr10-44407897;