1-199038079-C-T

Variant names:

• chr1-199038079-C-T
• rs7529925
• ENST00000432488.1:n.334-3477C>T

Variant summary

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

The ENST00000432488.1(LINC01221):​n.334-3477C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.764 in 151,900 control chromosomes in the GnomAD database, including 44,597 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 0.76 (44597 hom., cov: 31)
• Consequence: LINC01221 ENST00000432488.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17
• Publications: 21 publications found

Genes affected

LINC01221 (HGNC:49671): (long intergenic non-protein coding RNA 1221)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.84 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01221	NR_126351.1	n.334-3477C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01221	ENST00000432488.1	n.334-3477C>T		intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes AF: 0.764 AC: 115991 AN: 151782 Hom.: 44566 Cov.: 31

Gnomad AFR AF: 0.848

Gnomad AMI AF: 0.849

Gnomad AMR AF: 0.734

Gnomad ASJ AF: 0.718

Gnomad EAS AF: 0.808

Gnomad SAS AF: 0.713

Gnomad FIN AF: 0.724

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.728

Gnomad OTH AF: 0.767

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.764 AC: 116075 AN: 151900 Hom.: 44597 Cov.: 31 AF XY: 0.765 AC XY: 56779 AN XY: 74266

African (AFR) AF: 0.847 AC: 35139 AN: 41468

American (AMR) AF: 0.734 AC: 11177 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.718 AC: 2492 AN: 3472

East Asian (EAS) AF: 0.807 AC: 4169 AN: 5164

South Asian (SAS) AF: 0.713 AC: 3435 AN: 4820

European-Finnish (FIN) AF: 0.724 AC: 7636 AN: 10554

Middle Eastern (MID) AF: 0.735 AC: 216 AN: 294

European-Non Finnish (NFE) AF: 0.728 AC: 49415 AN: 67884

Other (OTH) AF: 0.769 AC: 1622 AN: 2108

Alfa AF: 0.744 Hom.: 69058

Bravo AF: 0.769

Asia WGS AF: 0.777 AC: 2701 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.074
DANN	Benign	0.22
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs7529925; hg19: chr1-199007208;