chr4-56690636-A-G

Variant names:

• chr4-56690636-A-G
• rs720428
• ENST00000848501.1:n.136+5958A>G

Variant summary

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

The ENST00000848501.1(ENSG00000310240):​n.136+5958A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.574 in 152,038 control chromosomes in the GnomAD database, including 25,977 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 0.57 (25977 hom., cov: 32)
• Consequence: ENSG00000310240 ENST00000848501.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0590
• Publications: 1 publications found

Genes affected

ENSG00000310240 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.64 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377666	XR_941078.3	n.314-5539A>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000310240	ENST00000848501.1	n.136+5958A>G		intron_variant	Intron 1 of 2
ENSG00000310240	ENST00000848502.1	n.171+5958A>G		intron_variant	Intron 1 of 2
ENSG00000310240	ENST00000848503.1	n.158+5958A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.574 AC: 87166 AN: 151920 Hom.: 25965 Cov.: 32

Gnomad AFR AF: 0.408

Gnomad AMI AF: 0.659

Gnomad AMR AF: 0.586

Gnomad ASJ AF: 0.652

Gnomad EAS AF: 0.654

Gnomad SAS AF: 0.620

Gnomad FIN AF: 0.660

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.645

Gnomad OTH AF: 0.559

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

GnomAD4 genome AF: 0.574 AC: 87220 AN: 152038 Hom.: 25977 Cov.: 32 AF XY: 0.576 AC XY: 42838 AN XY: 74328

African (AFR) AF: 0.407 AC: 16884 AN: 41448

American (AMR) AF: 0.586 AC: 8952 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.652 AC: 2262 AN: 3468

East Asian (EAS) AF: 0.655 AC: 3377 AN: 5152

South Asian (SAS) AF: 0.620 AC: 2987 AN: 4816

European-Finnish (FIN) AF: 0.660 AC: 6981 AN: 10582

Middle Eastern (MID) AF: 0.500 AC: 146 AN: 292

European-Non Finnish (NFE) AF: 0.645 AC: 43847 AN: 67982

Other (OTH) AF: 0.561 AC: 1183 AN: 2108

Alfa AF: 0.593 Hom.: 3523

Bravo AF: 0.562

Asia WGS AF: 0.613 AC: 2136 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	4.5
DANN	Benign	0.89
PhyloP100		-0.059

Splicing

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

Other links and lift over

dbSNP: rs720428; hg19: chr4-57556802;