rs7969151

Variant names:

• chr12-53765493-G-A
• rs7969151
• ENST00000652339.1:n.213+25605G>A

Variant summary

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

The ENST00000652339.1(ENSG00000286069):​n.213+25605G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.225 in 152,016 control chromosomes in the GnomAD database, including 4,420 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 (4420 hom., cov: 32)
• Consequence: ENSG00000286069 ENST00000652339.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.11
• Publications: 16 publications found

Genes affected

ENSG00000286069 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.343 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378250	NR_189097.1	n.295+25605G>A		intron_variant	Intron 1 of 2
LOC105378250	NR_189098.1	n.295+25605G>A		intron_variant	Intron 1 of 4
LOC105378250	NR_189099.1	n.295+25605G>A		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286069	ENST00000652339.1	n.213+25605G>A		intron_variant	Intron 1 of 4
ENSG00000286069	ENST00000654713.2	n.214+25605G>A		intron_variant	Intron 1 of 2
ENSG00000286069	ENST00000656247.1	n.143+14503G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.225 AC: 34184 AN: 151898 Hom.: 4416 Cov.: 32

Gnomad AFR AF: 0.348

Gnomad AMI AF: 0.286

Gnomad AMR AF: 0.203

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.0712

Gnomad SAS AF: 0.100

Gnomad FIN AF: 0.102

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.198

Gnomad OTH AF: 0.213

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

GnomAD4 genome AF: 0.225 AC: 34216 AN: 152016 Hom.: 4420 Cov.: 32 AF XY: 0.218 AC XY: 16175 AN XY: 74336

African (AFR) AF: 0.347 AC: 14385 AN: 41412

American (AMR) AF: 0.203 AC: 3100 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.175 AC: 605 AN: 3464

East Asian (EAS) AF: 0.0714 AC: 370 AN: 5182

South Asian (SAS) AF: 0.100 AC: 482 AN: 4812

European-Finnish (FIN) AF: 0.102 AC: 1074 AN: 10570

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.198 AC: 13445 AN: 67982

Other (OTH) AF: 0.210 AC: 443 AN: 2106

Alfa AF: 0.208 Hom.: 11019

Bravo AF: 0.240

Asia WGS AF: 0.116 AC: 405 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.020
DANN	Benign	0.22
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs7969151; hg19: chr12-54159277;