chr1-177753772-C-A

Variant names:

• chr1-177753772-C-A
• rs12140439
• ENST00000664407.1:n.72-4018G>T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000664407.1(ENSG00000227579):​n.72-4018G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.245 in 152,154 control chromosomes in the GnomAD database, including 5,506 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 0.25 (5506 hom., cov: 32)
• Consequence: ENSG00000227579 ENST00000664407.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.20

Genes affected

ENSG00000227579 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.32).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.322 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	ENST00000664407.1	n.72-4018G>T		intron_variant	Intron 1 of 6

Frequencies

GnomAD3 genomes AF: 0.245 AC: 37300 AN: 152036 Hom.: 5499 Cov.: 32

Gnomad AFR AF: 0.0904

Gnomad AMI AF: 0.288

Gnomad AMR AF: 0.262

Gnomad ASJ AF: 0.338

Gnomad EAS AF: 0.0845

Gnomad SAS AF: 0.286

Gnomad FIN AF: 0.331

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.326

Gnomad OTH AF: 0.262

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

GnomAD4 genome AF: 0.245 AC: 37316 AN: 152154 Hom.: 5506 Cov.: 32 AF XY: 0.245 AC XY: 18193 AN XY: 74382

Gnomad4 AFR AF: 0.0901

Gnomad4 AMR AF: 0.263

Gnomad4 ASJ AF: 0.338

Gnomad4 EAS AF: 0.0847

Gnomad4 SAS AF: 0.285

Gnomad4 FIN AF: 0.331

Gnomad4 NFE AF: 0.326

Gnomad4 OTH AF: 0.264

Alfa AF: 0.209 Hom.: 642

Bravo AF: 0.235

Asia WGS AF: 0.213 AC: 744 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.32
CADD	Benign	13
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12140439; hg19: chr1-177722907;