4-33652135-C-T

Variant names:

• chr4-33652135-C-T
• rs717947
• ENST00000673514.1:n.1365-41222C>T

Variant summary

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

The ENST00000673514.1(ENSG00000288321):​n.1365-41222C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.141 in 152,026 control chromosomes in the GnomAD database, including 1,907 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 0.14 (1907 hom., cov: 32)
• Consequence: ENSG00000288321 ENST00000673514.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.112
• Publications: 11 publications found

Genes affected

ENSG00000288321 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.319 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000673514.1. 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
	ENSG00000288321	ENST00000673514.1		n.1365-41222C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.141 AC: 21443 AN: 151908 Hom.: 1909 Cov.: 32

Gnomad AFR AF: 0.223

Gnomad AMI AF: 0.0329

Gnomad AMR AF: 0.155

Gnomad ASJ AF: 0.117

Gnomad EAS AF: 0.333

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.0841

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.0856

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.141 AC: 21446 AN: 152026 Hom.: 1907 Cov.: 32 AF XY: 0.145 AC XY: 10758 AN XY: 74302

African (AFR) AF: 0.223 AC: 9232 AN: 41458

American (AMR) AF: 0.155 AC: 2356 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.117 AC: 406 AN: 3468

East Asian (EAS) AF: 0.332 AC: 1709 AN: 5152

South Asian (SAS) AF: 0.139 AC: 672 AN: 4818

European-Finnish (FIN) AF: 0.0841 AC: 889 AN: 10572

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.0856 AC: 5823 AN: 68004

Other (OTH) AF: 0.137 AC: 290 AN: 2110

Alfa AF: 0.105 Hom.: 4271

Bravo AF: 0.151

Asia WGS AF: 0.258 AC: 895 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	3.6
DANN	Benign	0.79
PhyloP100		-0.11

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: rs717947;

hg19: chr4-33653757;