rs236233

Variant names:

• chr6-78415318-C-A
• rs236233
• ENST00000715178.1:n.903+72323G>T

Your query was ambiguous. Multiple possible variants found:

• chr6-78415318-C-A
• chr6-78415318-C-G

Variant summary

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

The ENST00000715178.1(ENSG00000230309):​n.903+72323G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.802 in 152,024 control chromosomes in the GnomAD database, including 49,165 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 0.80 (49165 hom., cov: 31)
• Consequence: ENSG00000230309 ENST00000715178.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.659
• Publications: 2 publications found

Genes affected

ENSG00000230309 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000715178.1. 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
	ENSG00000230309	ENST00000715178.1		n.903+72323G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.802 AC: 121854 AN: 151904 Hom.: 49118 Cov.: 31

Gnomad AFR AF: 0.789

Gnomad AMI AF: 0.788

Gnomad AMR AF: 0.805

Gnomad ASJ AF: 0.804

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.692

Gnomad FIN AF: 0.858

Gnomad MID AF: 0.640

Gnomad NFE AF: 0.795

Gnomad OTH AF: 0.781

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

GnomAD4 genome AF: 0.802 AC: 121961 AN: 152024 Hom.: 49165 Cov.: 31 AF XY: 0.802 AC XY: 59615 AN XY: 74298

African (AFR) AF: 0.789 AC: 32702 AN: 41436

American (AMR) AF: 0.805 AC: 12299 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.804 AC: 2791 AN: 3470

East Asian (EAS) AF: 0.998 AC: 5170 AN: 5182

South Asian (SAS) AF: 0.691 AC: 3322 AN: 4810

European-Finnish (FIN) AF: 0.858 AC: 9068 AN: 10574

Middle Eastern (MID) AF: 0.640 AC: 187 AN: 292

European-Non Finnish (NFE) AF: 0.795 AC: 54051 AN: 67968

Other (OTH) AF: 0.784 AC: 1654 AN: 2110

Alfa AF: 0.787 Hom.: 109272

Bravo AF: 0.803

Asia WGS AF: 0.865 AC: 3008 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.89
DANN	Benign	0.51
PhyloP100		-0.66

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: rs236233;

hg19: chr6-79125035;