4-156142163-G-C

Variant names:

• chr4-156142163-G-C
• rs7670748
• ENST00000815672.1:n.366+1589C>G

Variant summary

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

The ENST00000815672.1(ENSG00000306151):​n.366+1589C>G 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 152,128 control chromosomes in the GnomAD database, including 54,146 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 (54146 hom., cov: 32)
• Consequence: ENSG00000306151 ENST00000815672.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.837
• Publications: 3 publications found

Genes affected

ENSG00000306151 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.882 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000815672.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000306151	ENST00000815672.1		n.366+1589C>G		intron	N/A
	ENSG00000306151	ENST00000815673.1		n.252+1589C>G		intron	N/A
	ENSG00000306151	ENST00000815674.1		n.191+1589C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.842 AC: 127921 AN: 152010 Hom.: 54110 Cov.: 32

Gnomad AFR AF: 0.798

Gnomad AMI AF: 0.912

Gnomad AMR AF: 0.730

Gnomad ASJ AF: 0.831

Gnomad EAS AF: 0.866

Gnomad SAS AF: 0.790

Gnomad FIN AF: 0.882

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.888

Gnomad OTH AF: 0.847

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

GnomAD4 genome AF: 0.841 AC: 128000 AN: 152128 Hom.: 54146 Cov.: 32 AF XY: 0.837 AC XY: 62249 AN XY: 74368

African (AFR) AF: 0.797 AC: 33065 AN: 41482

American (AMR) AF: 0.729 AC: 11137 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.831 AC: 2884 AN: 3472

East Asian (EAS) AF: 0.867 AC: 4492 AN: 5184

South Asian (SAS) AF: 0.792 AC: 3812 AN: 4814

European-Finnish (FIN) AF: 0.882 AC: 9339 AN: 10584

Middle Eastern (MID) AF: 0.820 AC: 241 AN: 294

European-Non Finnish (NFE) AF: 0.888 AC: 60409 AN: 68002

Other (OTH) AF: 0.846 AC: 1789 AN: 2114

Alfa AF: 0.864 Hom.: 6732

Bravo AF: 0.832

Asia WGS AF: 0.838 AC: 2915 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.67
DANN	Benign	0.76
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs7670748; hg19: chr4-157063315;