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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000423193.2. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000224239	ENST00000423193.2	TSL:2	n.447C>T		non_coding_transcript_exon	Exon 1 of 2
	LINC01266	ENST00000794129.1		n.539-12981C>T		intron	N/A
	LINC01266	ENST00000794142.1		n.511-12981C>T		intron	N/A

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 v4.9

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

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

Other links and lift over

dbSNP: rs35964523;

hg19: chr3-898661;