10-42980330-T-G

Variant names:

• chr10-42980330-T-G
• rs11239851
• ENST00000431395.1:n.370A>C

Variant summary

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

The ENST00000431395.1(LINC01264):​n.370A>C 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 0.256 in 152,216 control chromosomes in the GnomAD database, including 5,194 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 0.26 (5191 hom., cov: 33)
  • Exomes 𝑓: 0.39 (3 hom.)
• Consequence: LINC01264 ENST00000431395.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.115
• Publications: 2 publications found

Genes affected

LINC01264 (HGNC:50282): (long intergenic non-protein coding RNA 1264)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.282 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01264	NR_126352.1	n.370A>C		non_coding_transcript_exon_variant	Exon 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01264	ENST00000431395.1	n.370A>C		non_coding_transcript_exon_variant	Exon 2 of 3	3
LINC01264	ENST00000754421.1	n.630+1038A>C		intron_variant	Intron 2 of 2
LINC01264	ENST00000754422.1	n.299+1038A>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.256 AC: 38862 AN: 152052 Hom.: 5179 Cov.: 33

Gnomad AFR AF: 0.286

Gnomad AMI AF: 0.224

Gnomad AMR AF: 0.216

Gnomad ASJ AF: 0.336

Gnomad EAS AF: 0.00174

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.280

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.265

Gnomad OTH AF: 0.253

GnomAD4 exome AF: 0.391 AC: 18 AN: 46 Hom.: 3 Cov.: 0 AF XY: 0.412 AC XY: 14 AN XY: 34

African (AFR) AF: 0.00 AC: 0 AN: 4

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) AF: 0.500 AC: 1 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.447 AC: 17 AN: 38

Other (OTH) AF: 0.00 AC: 0 AN: 2

GnomAD4 genome AF: 0.256 AC: 38906 AN: 152170 Hom.: 5191 Cov.: 33 AF XY: 0.252 AC XY: 18746 AN XY: 74394

African (AFR) AF: 0.286 AC: 11888 AN: 41526

American (AMR) AF: 0.216 AC: 3302 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.336 AC: 1167 AN: 3472

East Asian (EAS) AF: 0.00174 AC: 9 AN: 5174

South Asian (SAS) AF: 0.152 AC: 733 AN: 4824

European-Finnish (FIN) AF: 0.280 AC: 2966 AN: 10578

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.265 AC: 18026 AN: 67976

Other (OTH) AF: 0.250 AC: 529 AN: 2114

Alfa AF: 0.171 Hom.: 385

Bravo AF: 0.253

Asia WGS AF: 0.100 AC: 353 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.4
DANN	Benign	0.31
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs11239851; hg19: chr10-43475778;