chr1-56488267-A-G

Variant names:

• chr1-56488267-A-G
• rs7532239
• ENST00000642129.1:n.576-4813T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

Genes affected

ENSG00000284686 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000284686	ENST00000642129.1	n.576-4813T>C		intron_variant	Intron 4 of 5			ENSP00000492927.1
ENSG00000284686	ENST00000641109.1	n.342-4813T>C		intron_variant	Intron 3 of 5			ENSP00000493138.1
ENSG00000284686	ENST00000641494.1	n.186-4813T>C		intron_variant	Intron 2 of 5			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

African (AFR) AF: 0.747 AC: 30989 AN: 41466

American (AMR) AF: 0.612 AC: 9345 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.683 AC: 2371 AN: 3472

East Asian (EAS) AF: 0.435 AC: 2251 AN: 5174

South Asian (SAS) AF: 0.471 AC: 2274 AN: 4826

European-Finnish (FIN) AF: 0.615 AC: 6491 AN: 10558

Middle Eastern (MID) AF: 0.741 AC: 218 AN: 294

European-Non Finnish (NFE) AF: 0.686 AC: 46630 AN: 67986

Other (OTH) AF: 0.665 AC: 1407 AN: 2116

Alfa AF: 0.673 Hom.: 6093

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
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs7532239; hg19: chr1-56953939;