rs722832

Variant names:

• chr4-177219788-T-A
• rs722832
• ENST00000656694.1:n.301+699A>T

Variant summary

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

The ENST00000656694.1(ENSG00000287544):​n.301+699A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.601 in 151,980 control chromosomes in the GnomAD database, including 31,989 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 0.60 (31989 hom., cov: 31)
• Consequence: ENSG00000287544 ENST00000656694.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.545
• Publications: 1 publications found

Genes affected

ENSG00000287544 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.791 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000656694.1. 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
	ENSG00000287544	ENST00000656694.1		n.301+699A>T		intron	N/A
	ENSG00000287544	ENST00000662794.1		n.374+699A>T		intron	N/A
	ENSG00000287544	ENST00000667713.1		n.396+699A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.601 AC: 91268 AN: 151860 Hom.: 31983 Cov.: 31

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.873

Gnomad AMR AF: 0.635

Gnomad ASJ AF: 0.784

Gnomad EAS AF: 0.219

Gnomad SAS AF: 0.639

Gnomad FIN AF: 0.708

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.797

Gnomad OTH AF: 0.653

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

GnomAD4 genome AF: 0.601 AC: 91285 AN: 151980 Hom.: 31989 Cov.: 31 AF XY: 0.596 AC XY: 44230 AN XY: 74272

African (AFR) AF: 0.257 AC: 10654 AN: 41440

American (AMR) AF: 0.635 AC: 9703 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.784 AC: 2716 AN: 3466

East Asian (EAS) AF: 0.220 AC: 1134 AN: 5164

South Asian (SAS) AF: 0.640 AC: 3078 AN: 4808

European-Finnish (FIN) AF: 0.708 AC: 7467 AN: 10552

Middle Eastern (MID) AF: 0.687 AC: 202 AN: 294

European-Non Finnish (NFE) AF: 0.797 AC: 54170 AN: 67964

Other (OTH) AF: 0.647 AC: 1365 AN: 2110

Alfa AF: 0.686 Hom.: 4810

Bravo AF: 0.581

Asia WGS AF: 0.432 AC: 1506 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.3
DANN	Benign	0.65
PhyloP100		-0.55

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: rs722832;

hg19: chr4-178140942;