7-91314953-C-G

Variant names:

• chr7-91314953-C-G
• rs1429524
• ENST00000418395.1:n.124-1020C>G

Variant summary

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

The ENST00000418395.1(LINC02932):​n.124-1020C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.417 in 151,924 control chromosomes in the GnomAD database, including 14,479 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 0.42 (14479 hom., cov: 32)
• Consequence: LINC02932 ENST00000418395.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.402
• Publications: 5 publications found

Genes affected

LINC02932 (HGNC:55875): (long intergenic non-protein coding RNA 2932)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.596 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02932	NR_183366.1	n.186-1020C>G		intron_variant	Intron 2 of 6
LINC02932	NR_183367.1	n.186-1020C>G		intron_variant	Intron 2 of 4
LINC02932	NR_183376.1	n.186-1020C>G		intron_variant	Intron 2 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02932	ENST00000418395.1	n.124-1020C>G		intron_variant	Intron 1 of 5	3
LINC02932	ENST00000419226.5	n.124-1020C>G		intron_variant	Intron 1 of 4	3
LINC02932	ENST00000449361.5	n.143-1020C>G		intron_variant	Intron 2 of 5	5

Frequencies

GnomAD3 genomes AF: 0.417 AC: 63289 AN: 151806 Hom.: 14447 Cov.: 32

Gnomad AFR AF: 0.597

Gnomad AMI AF: 0.536

Gnomad AMR AF: 0.410

Gnomad ASJ AF: 0.328

Gnomad EAS AF: 0.614

Gnomad SAS AF: 0.344

Gnomad FIN AF: 0.334

Gnomad MID AF: 0.394

Gnomad NFE AF: 0.315

Gnomad OTH AF: 0.420

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

GnomAD4 genome AF: 0.417 AC: 63374 AN: 151924 Hom.: 14479 Cov.: 32 AF XY: 0.418 AC XY: 31027 AN XY: 74240

African (AFR) AF: 0.598 AC: 24783 AN: 41458

American (AMR) AF: 0.410 AC: 6257 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.328 AC: 1137 AN: 3470

East Asian (EAS) AF: 0.614 AC: 3162 AN: 5148

South Asian (SAS) AF: 0.343 AC: 1653 AN: 4818

European-Finnish (FIN) AF: 0.334 AC: 3517 AN: 10518

Middle Eastern (MID) AF: 0.383 AC: 111 AN: 290

European-Non Finnish (NFE) AF: 0.315 AC: 21379 AN: 67940

Other (OTH) AF: 0.420 AC: 886 AN: 2110

Alfa AF: 0.379 Hom.: 1417

Bravo AF: 0.435

Asia WGS AF: 0.462 AC: 1603 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	3.4
DANN	Benign	0.59
PhyloP100		0.40

Splicing

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

Other links and lift over

dbSNP: rs1429524; hg19: chr7-90944268;