4-133565856-G-C

Variant names:

• chr4-133565856-G-C
• rs9307696
• ENST00000721553.1:n.347+10401G>C

Variant summary

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

The ENST00000721553.1(ENSG00000294158):​n.347+10401G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.662 in 152,036 control chromosomes in the GnomAD database, including 33,690 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 0.66 (33690 hom., cov: 32)
• Consequence: ENSG00000294158 ENST00000721553.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.90
• Publications: 4 publications found

Genes affected

ENSG00000294158 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.747 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000721553.1. 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
	ENSG00000294158	ENST00000721553.1		n.347+10401G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.661 AC: 100477 AN: 151916 Hom.: 33640 Cov.: 32

Gnomad AFR AF: 0.753

Gnomad AMI AF: 0.586

Gnomad AMR AF: 0.603

Gnomad ASJ AF: 0.544

Gnomad EAS AF: 0.728

Gnomad SAS AF: 0.505

Gnomad FIN AF: 0.704

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.627

Gnomad OTH AF: 0.624

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

GnomAD4 genome AF: 0.662 AC: 100583 AN: 152036 Hom.: 33690 Cov.: 32 AF XY: 0.659 AC XY: 49008 AN XY: 74316

African (AFR) AF: 0.754 AC: 31262 AN: 41488

American (AMR) AF: 0.603 AC: 9199 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.544 AC: 1886 AN: 3468

East Asian (EAS) AF: 0.728 AC: 3758 AN: 5160

South Asian (SAS) AF: 0.504 AC: 2429 AN: 4824

European-Finnish (FIN) AF: 0.704 AC: 7432 AN: 10560

Middle Eastern (MID) AF: 0.565 AC: 166 AN: 294

European-Non Finnish (NFE) AF: 0.627 AC: 42596 AN: 67958

Other (OTH) AF: 0.625 AC: 1321 AN: 2112

Alfa AF: 0.517 Hom.: 1419

Bravo AF: 0.663

Asia WGS AF: 0.639 AC: 2220 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.17
DANN	Benign	0.46
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs9307696; hg19: chr4-134487011;