1-234738993-C-G

Variant names:

• chr1-234738993-C-G
• rs7554650
• ENST00000762106.1:n.219-4588C>G

Variant summary

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

The ENST00000762106.1(LINC01132):​n.219-4588C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.349 in 152,088 control chromosomes in the GnomAD database, including 11,219 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 0.35 (11219 hom., cov: 32)
• Consequence: LINC01132 ENST00000762106.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.163
• Publications: 2 publications found

Genes affected

LINC01132 (HGNC:49444): (long intergenic non-protein coding RNA 1132)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.483 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
LINC01132	ENST00000762106.1	n.219-4588C>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.350 AC: 53144 AN: 151970 Hom.: 11233 Cov.: 32

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.442

Gnomad AMR AF: 0.318

Gnomad ASJ AF: 0.475

Gnomad EAS AF: 0.258

Gnomad SAS AF: 0.324

Gnomad FIN AF: 0.417

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.487

Gnomad OTH AF: 0.398

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

GnomAD4 genome AF: 0.349 AC: 53126 AN: 152088 Hom.: 11219 Cov.: 32 AF XY: 0.347 AC XY: 25770 AN XY: 74350

African (AFR) AF: 0.117 AC: 4852 AN: 41510

American (AMR) AF: 0.318 AC: 4856 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.475 AC: 1649 AN: 3470

East Asian (EAS) AF: 0.258 AC: 1337 AN: 5180

South Asian (SAS) AF: 0.323 AC: 1560 AN: 4824

European-Finnish (FIN) AF: 0.417 AC: 4402 AN: 10560

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.487 AC: 33111 AN: 67958

Other (OTH) AF: 0.397 AC: 840 AN: 2114

Alfa AF: 0.287 Hom.: 843

Bravo AF: 0.330

Asia WGS AF: 0.287 AC: 998 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.1
DANN	Benign	0.67
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs7554650; hg19: chr1-234874740;