rs7527462

Variant names:

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

Variant summary

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

The ENST00000432694.2(ENSG00000224000):​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: ENSG00000224000 ENST00000432694.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.261
• Publications: 9 publications found

Genes affected

ENSG00000224000 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000432694.2. 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
	ENSG00000224000	ENST00000432694.2	TSL:3	n.224-111042C>G		intron	N/A
	ENSG00000224000	ENST00000717047.1		n.354-6726C>G		intron	N/A
	ENSG00000224000	ENST00000717048.1		n.323+9541C>G		intron	N/A

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

African (AFR) AF: 0.334 AC: 13834 AN: 41432

American (AMR) AF: 0.464 AC: 7088 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.264 AC: 914 AN: 3468

East Asian (EAS) AF: 0.895 AC: 4617 AN: 5158

South Asian (SAS) AF: 0.416 AC: 1999 AN: 4804

European-Finnish (FIN) AF: 0.295 AC: 3117 AN: 10556

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.239 AC: 16265 AN: 67962

Other (OTH) AF: 0.325 AC: 686 AN: 2110

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.6
DANN	Benign	0.74
PhyloP100		0.26

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: rs7527462;

hg19: chr1-172862380;