rs7721001

Variant names:

• chr5-159223806-C-T
• rs7721001
• ENST00000521204.2:n.231+12786C>T

Variant summary

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

The ENST00000521204.2(LINC01932):​n.231+12786C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.549 in 152,024 control chromosomes in the GnomAD database, including 24,330 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 0.55 (24330 hom., cov: 32)
• Consequence: LINC01932 ENST00000521204.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.723
• Publications: 4 publications found

Genes affected

LINC01932 (HGNC:52755): (long intergenic non-protein coding RNA 1932)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.745 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01932	ENST00000521204.2	n.231+12786C>T		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes AF: 0.549 AC: 83419 AN: 151906 Hom.: 24295 Cov.: 32

Gnomad AFR AF: 0.752

Gnomad AMI AF: 0.582

Gnomad AMR AF: 0.557

Gnomad ASJ AF: 0.465

Gnomad EAS AF: 0.431

Gnomad SAS AF: 0.578

Gnomad FIN AF: 0.398

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.458

Gnomad OTH AF: 0.561

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

GnomAD4 genome AF: 0.549 AC: 83505 AN: 152024 Hom.: 24330 Cov.: 32 AF XY: 0.547 AC XY: 40649 AN XY: 74308

African (AFR) AF: 0.752 AC: 31161 AN: 41450

American (AMR) AF: 0.557 AC: 8512 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.465 AC: 1614 AN: 3472

East Asian (EAS) AF: 0.431 AC: 2226 AN: 5160

South Asian (SAS) AF: 0.577 AC: 2778 AN: 4818

European-Finnish (FIN) AF: 0.398 AC: 4200 AN: 10556

Middle Eastern (MID) AF: 0.554 AC: 163 AN: 294

European-Non Finnish (NFE) AF: 0.458 AC: 31133 AN: 67972

Other (OTH) AF: 0.562 AC: 1187 AN: 2112

Alfa AF: 0.500 Hom.: 56633

Bravo AF: 0.568

Asia WGS AF: 0.533 AC: 1853 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	1.1
DANN	Benign	0.91
PhyloP100		-0.72

Splicing

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

Other links and lift over

dbSNP: rs7721001; hg19: chr5-158650814;