rs35964523

Variant names:

• chr3-856978-C-T
• rs35964523
• ENST00000423193.2:n.447C>T

Variant summary

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

The ENST00000423193.2(ENSG00000224239):​n.447C>T 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 0.362 in 151,832 control chromosomes in the GnomAD database, including 10,169 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 0.36 (10169 hom., cov: 33)
  • Exomes 𝑓: 0.25 (0 hom.)
• Consequence: ENSG00000224239 ENST00000423193.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00
• Publications: 8 publications found

Genes affected

ENSG00000224239 (HGNC:):

LINC01266 (HGNC:50309): (long intergenic non-protein coding RNA 1266)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.534 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986058	XR_001740584.1	n.1837C>T		non_coding_transcript_exon_variant	Exon 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000224239	ENST00000423193.2	n.447C>T		non_coding_transcript_exon_variant	Exon 1 of 2	2
LINC01266	ENST00000794129.1	n.539-12981C>T		intron_variant	Intron 6 of 6
LINC01266	ENST00000794142.1	n.511-12981C>T		intron_variant	Intron 5 of 5

Frequencies

GnomAD3 genomes AF: 0.362 AC: 54972 AN: 151710 Hom.: 10175 Cov.: 33

Gnomad AFR AF: 0.313

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.427

Gnomad ASJ AF: 0.299

Gnomad EAS AF: 0.550

Gnomad SAS AF: 0.466

Gnomad FIN AF: 0.356

Gnomad MID AF: 0.414

Gnomad NFE AF: 0.361

Gnomad OTH AF: 0.378

GnomAD4 exome AF: 0.250 AC: 1 AN: 4 Hom.: 0 AF XY: 0.250 AC XY: 1 AN XY: 4

African (AFR) AC: 0 AN: 0

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: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.500 AC: 1 AN: 2

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.362 AC: 54988 AN: 151828 Hom.: 10169 Cov.: 33 AF XY: 0.366 AC XY: 27141 AN XY: 74180

African (AFR) AF: 0.313 AC: 12964 AN: 41460

American (AMR) AF: 0.427 AC: 6511 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.299 AC: 1038 AN: 3472

East Asian (EAS) AF: 0.551 AC: 2823 AN: 5128

South Asian (SAS) AF: 0.464 AC: 2225 AN: 4800

European-Finnish (FIN) AF: 0.356 AC: 3752 AN: 10526

Middle Eastern (MID) AF: 0.414 AC: 121 AN: 292

European-Non Finnish (NFE) AF: 0.361 AC: 24510 AN: 67876

Other (OTH) AF: 0.382 AC: 807 AN: 2112

Alfa AF: 0.368 Hom.: 14554

Bravo AF: 0.361

Asia WGS AF: 0.504 AC: 1749 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.19
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs35964523; hg19: chr3-898661;