1-177464440-A-G

Variant names:

• chr1-177464440-A-G
• rs12026256
• ENST00000438575.7:n.389-70652T>C

Variant summary

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

The ENST00000438575.7(ENSG00000227579):​n.389-70652T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0647 in 152,156 control chromosomes in the GnomAD database, including 1,217 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 0.065 (1217 hom., cov: 32)
• Consequence: ENSG00000227579 ENST00000438575.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.671
• Publications: 1 publications found

Genes affected

ENSG00000227579 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.561 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000438575.7. 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
	ENSG00000227579	ENST00000438575.7	TSL:3	n.389-70652T>C		intron	N/A
	ENSG00000227579	ENST00000458070.1	TSL:5	n.437-70652T>C		intron	N/A
	ENSG00000227579	ENST00000654501.1		n.196-70652T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0646 AC: 9820 AN: 152038 Hom.: 1211 Cov.: 32

Gnomad AFR AF: 0.0804

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0715

Gnomad ASJ AF: 0.0187

Gnomad EAS AF: 0.579

Gnomad SAS AF: 0.179

Gnomad FIN AF: 0.0828

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.00756

Gnomad OTH AF: 0.0445

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

GnomAD4 genome AF: 0.0647 AC: 9841 AN: 152156 Hom.: 1217 Cov.: 32 AF XY: 0.0728 AC XY: 5417 AN XY: 74378

African (AFR) AF: 0.0801 AC: 3327 AN: 41534

American (AMR) AF: 0.0720 AC: 1101 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0187 AC: 65 AN: 3468

East Asian (EAS) AF: 0.579 AC: 2968 AN: 5130

South Asian (SAS) AF: 0.180 AC: 865 AN: 4816

European-Finnish (FIN) AF: 0.0828 AC: 878 AN: 10608

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.00756 AC: 514 AN: 67996

Other (OTH) AF: 0.0545 AC: 115 AN: 2112

Alfa AF: 0.0337 Hom.: 1144

Bravo AF: 0.0651

Asia WGS AF: 0.368 AC: 1277 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	12
DANN	Benign	0.76
PhyloP100		0.67

Splicing

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

Other links and lift over

dbSNP: rs12026256; hg19: chr1-177433576;