rs720428

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr4-56690636-A-G
• chr4-56690636-A-T

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000848501.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000310240	ENST00000848501.1		n.136+5958A>G		intron	N/A
	ENSG00000310240	ENST00000848502.1		n.171+5958A>G		intron	N/A
	ENSG00000310240	ENST00000848503.1		n.158+5958A>G		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs720428;

hg19: chr4-57556802;