1-12218875-A-G

Variant names:

• chr1-12218875-A-G
• rs7550488
• ENST00000744993.1:n.534+1074A>G

Variant summary

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

The ENST00000744993.1(ENSG00000297053):​n.534+1074A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.767 in 151,886 control chromosomes in the GnomAD database, including 44,675 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 0.77 (44675 hom., cov: 29)
• Consequence: ENSG00000297053 ENST00000744993.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.773
• Publications: 11 publications found

Genes affected

ENSG00000297053 (HGNC:):

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 (AMR) allele frequency at 95% confidence interval = 0.785 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000744993.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000297053	ENST00000744993.1		n.534+1074A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.767 AC: 116334 AN: 151766 Hom.: 44640 Cov.: 29

Gnomad AFR AF: 0.782

Gnomad AMI AF: 0.765

Gnomad AMR AF: 0.797

Gnomad ASJ AF: 0.726

Gnomad EAS AF: 0.595

Gnomad SAS AF: 0.768

Gnomad FIN AF: 0.720

Gnomad MID AF: 0.709

Gnomad NFE AF: 0.773

Gnomad OTH AF: 0.779

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

GnomAD4 genome AF: 0.767 AC: 116425 AN: 151886 Hom.: 44675 Cov.: 29 AF XY: 0.763 AC XY: 56661 AN XY: 74242

African (AFR) AF: 0.781 AC: 32360 AN: 41408

American (AMR) AF: 0.797 AC: 12160 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.726 AC: 2518 AN: 3468

East Asian (EAS) AF: 0.595 AC: 3059 AN: 5144

South Asian (SAS) AF: 0.768 AC: 3697 AN: 4814

European-Finnish (FIN) AF: 0.720 AC: 7604 AN: 10558

Middle Eastern (MID) AF: 0.697 AC: 205 AN: 294

European-Non Finnish (NFE) AF: 0.773 AC: 52485 AN: 67928

Other (OTH) AF: 0.779 AC: 1642 AN: 2108

Alfa AF: 0.771 Hom.: 77976

Bravo AF: 0.773

Asia WGS AF: 0.697 AC: 2424 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.2
DANN	Benign	0.73
PhyloP100		-0.77

Splicing

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

Other links and lift over

dbSNP: rs7550488; hg19: chr1-12278932; COSMIC: COSV71768863;