rs7527462

Variant names:

• chr1-172893240-C-G
• rs7527462
• ENST00000432694.2:n.224-111042C>G

Variant summary

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

The ENST00000432694.2(ENSG00000224228):​n.224-111042C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.321 in 151,970 control chromosomes in the GnomAD database, including 9,221 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 0.32 (9221 hom., cov: 31)
• Consequence: ENSG00000224228 ENST00000432694.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.261

Genes affected

ENSG00000224228 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.874 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
ENSG00000224228	ENST00000432694.2	n.224-111042C>G		intron_variant	Intron 1 of 4	3

Frequencies

GnomAD3 genomes AF: 0.321 AC: 48738 AN: 151852 Hom.: 9217 Cov.: 31

Gnomad AFR AF: 0.334

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.463

Gnomad ASJ AF: 0.264

Gnomad EAS AF: 0.896

Gnomad SAS AF: 0.416

Gnomad FIN AF: 0.295

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.239

Gnomad OTH AF: 0.328

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

GnomAD4 genome AF: 0.321 AC: 48759 AN: 151970 Hom.: 9221 Cov.: 31 AF XY: 0.330 AC XY: 24483 AN XY: 74280

Gnomad4 AFR AF: 0.334

Gnomad4 AMR AF: 0.464

Gnomad4 ASJ AF: 0.264

Gnomad4 EAS AF: 0.895

Gnomad4 SAS AF: 0.416

Gnomad4 FIN AF: 0.295

Gnomad4 NFE AF: 0.239

Gnomad4 OTH AF: 0.325

Alfa AF: 0.276 Hom.: 786

Bravo AF: 0.344

Asia WGS AF: 0.562 AC: 1954 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.6
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7527462; hg19: chr1-172862380;