rs7964748

Positions:

• chr12-102571551-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007063427.1(LINC02456):​n.34902+87663A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.226 in 151,922 control chromosomes in the GnomAD database, including 4,031 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 0.23 (4031 hom., cov: 31)
• Consequence: LINC02456 XR_007063427.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.135

Genes affected

LINC02456 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.293 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02456	XR_007063427.1	n.34902+87663A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.226 AC: 34302 AN: 151804 Hom.: 4021 Cov.: 31

Gnomad AFR AF: 0.297

Gnomad AMI AF: 0.247

Gnomad AMR AF: 0.186

Gnomad ASJ AF: 0.200

Gnomad EAS AF: 0.177

Gnomad SAS AF: 0.284

Gnomad FIN AF: 0.231

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.191

Gnomad OTH AF: 0.225

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

GnomAD4 genome AF: 0.226 AC: 34341 AN: 151922 Hom.: 4031 Cov.: 31 AF XY: 0.229 AC XY: 16970 AN XY: 74244

Gnomad4 AFR AF: 0.297

Gnomad4 AMR AF: 0.186

Gnomad4 ASJ AF: 0.200

Gnomad4 EAS AF: 0.177

Gnomad4 SAS AF: 0.284

Gnomad4 FIN AF: 0.231

Gnomad4 NFE AF: 0.191

Gnomad4 OTH AF: 0.221

Alfa AF: 0.206 Hom.: 1496

Bravo AF: 0.223

Asia WGS AF: 0.215 AC: 747 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.5
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7964748; hg19: chr12-102965329;