1-56488267-A-G

Position:

• chr1-56488267-A-G

Variant summary

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

The ENST00000642129.1(ENSG00000284686):​n.576-4813T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.675 in 152,084 control chromosomes in the GnomAD database, including 35,085 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 0.67 (35085 hom., cov: 32)
• Consequence: ENSG00000284686 ENST00000642129.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.447

Genes affected

ENSG00000284686 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.74 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.56488267A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000284686	ENST00000642129.1	n.576-4813T>C		intron_variant				ENSP00000492927.1
ENSG00000284686	ENST00000641109.1	n.342-4813T>C		intron_variant				ENSP00000493138.1
ENSG00000284686	ENST00000641494.1	n.186-4813T>C		intron_variant				ENSP00000492970.1

Frequencies

GnomAD3 genomes AF: 0.675 AC: 102572 AN: 151966 Hom.: 35070 Cov.: 32

Gnomad AFR AF: 0.748

Gnomad AMI AF: 0.720

Gnomad AMR AF: 0.612

Gnomad ASJ AF: 0.683

Gnomad EAS AF: 0.435

Gnomad SAS AF: 0.471

Gnomad FIN AF: 0.615

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.686

Gnomad OTH AF: 0.670

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

GnomAD4 genome AF: 0.675 AC: 102633 AN: 152084 Hom.: 35085 Cov.: 32 AF XY: 0.667 AC XY: 49633 AN XY: 74360

Gnomad4 AFR AF: 0.747

Gnomad4 AMR AF: 0.612

Gnomad4 ASJ AF: 0.683

Gnomad4 EAS AF: 0.435

Gnomad4 SAS AF: 0.471

Gnomad4 FIN AF: 0.615

Gnomad4 NFE AF: 0.686

Gnomad4 OTH AF: 0.665

Alfa AF: 0.671 Hom.: 5878

Bravo AF: 0.678

Asia WGS AF: 0.443 AC: 1546 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.7
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7532239; hg19: chr1-56953939;