rs7964748

Variant names:

• chr12-102571551-A-G
• rs7964748
• ENST00000737486.1:n.121+27185A>G

Variant summary

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

The ENST00000737486.1(ENSG00000296233):​n.121+27185A>G variant causes a intron 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: ENSG00000296233 ENST00000737486.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.135
• Publications: 5 publications found

Genes affected

ENSG00000296233 (HGNC:):

LINC02456 (HGNC:53389): (long intergenic non-protein coding RNA 2456)

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000737486.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000296233	ENST00000737486.1		n.121+27185A>G		intron	N/A
	ENSG00000296233	ENST00000737487.1		n.121+27185A>G		intron	N/A

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

African (AFR) AF: 0.297 AC: 12321 AN: 41436

American (AMR) AF: 0.186 AC: 2836 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.200 AC: 694 AN: 3462

East Asian (EAS) AF: 0.177 AC: 909 AN: 5146

South Asian (SAS) AF: 0.284 AC: 1365 AN: 4806

European-Finnish (FIN) AF: 0.231 AC: 2433 AN: 10520

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.191 AC: 13001 AN: 67970

Other (OTH) AF: 0.221 AC: 465 AN: 2102

Alfa AF: 0.204 Hom.: 6501

Bravo AF: 0.223

Asia WGS AF: 0.215 AC: 747 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.5
DANN	Benign	0.51
PhyloP100		-0.14

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7964748;

hg19: chr12-102965329;