1-177464440-A-G

Variant names:

• chr1-177464440-A-G
• rs12026256
• ENST00000438575.6:n.374-70652T>C

Variant summary

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

The ENST00000438575.6(ENSG00000227579):​n.374-70652T>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 ENST00000438575.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.671

Genes affected

ENSG00000227579 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

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
ENSG00000227579	ENST00000438575.6	n.374-70652T>C		intron_variant	Intron 3 of 3	3
ENSG00000227579	ENST00000458070.1	n.437-70652T>C		intron_variant	Intron 3 of 3	5
ENSG00000227579	ENST00000654501.1	n.196-70652T>C		intron_variant	Intron 2 of 2

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

Gnomad4 AFR AF: 0.0801

Gnomad4 AMR AF: 0.0720

Gnomad4 ASJ AF: 0.0187

Gnomad4 EAS AF: 0.579

Gnomad4 SAS AF: 0.180

Gnomad4 FIN AF: 0.0828

Gnomad4 NFE AF: 0.00756

Gnomad4 OTH AF: 0.0545

Alfa AF: 0.0316 Hom.: 144

Bravo AF: 0.0651

Asia WGS AF: 0.368 AC: 1277 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12026256; hg19: chr1-177433576;