rs4947882

Variant names:

• chr7-54190442-G-T
• rs4947882
• ENST00000657889.1:n.323-3651C>A

Variant summary

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

The ENST00000657889.1(ENSG00000287953):​n.323-3651C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.841 in 151,956 control chromosomes in the GnomAD database, including 55,951 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 0.84 (55951 hom., cov: 32)
• Consequence: ENSG00000287953 ENST00000657889.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.723
• Publications: 0 publications found

Genes affected

ENSG00000287953 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.961 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000657889.1. 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
	ENSG00000287953	ENST00000657889.1		n.323-3651C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.841 AC: 127692 AN: 151840 Hom.: 55933 Cov.: 32

Gnomad AFR AF: 0.571

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.909

Gnomad ASJ AF: 0.963

Gnomad EAS AF: 0.776

Gnomad SAS AF: 0.896

Gnomad FIN AF: 0.930

Gnomad MID AF: 0.905

Gnomad NFE AF: 0.967

Gnomad OTH AF: 0.875

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

GnomAD4 genome AF: 0.841 AC: 127743 AN: 151956 Hom.: 55951 Cov.: 32 AF XY: 0.839 AC XY: 62354 AN XY: 74280

African (AFR) AF: 0.570 AC: 23587 AN: 41346

American (AMR) AF: 0.909 AC: 13875 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.963 AC: 3344 AN: 3472

East Asian (EAS) AF: 0.777 AC: 4008 AN: 5158

South Asian (SAS) AF: 0.896 AC: 4310 AN: 4810

European-Finnish (FIN) AF: 0.930 AC: 9828 AN: 10572

Middle Eastern (MID) AF: 0.901 AC: 265 AN: 294

European-Non Finnish (NFE) AF: 0.967 AC: 65763 AN: 68022

Other (OTH) AF: 0.876 AC: 1851 AN: 2114

Alfa AF: 0.881 Hom.: 7875

Bravo AF: 0.827

Asia WGS AF: 0.827 AC: 2880 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.34
DANN	Benign	0.34
PhyloP100		-0.72

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: rs4947882;

hg19: chr7-54258135;