6-78224383-C-T

Variant names:

• chr6-78224383-C-T
• rs2050689
• ENST00000715178.1:n.1038-20430G>A

Variant summary

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

The ENST00000715178.1(ENSG00000230309):​n.1038-20430G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.121 in 150,532 control chromosomes in the GnomAD database, including 1,149 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 0.12 (1149 hom., cov: 31)
• Consequence: ENSG00000230309 ENST00000715178.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.428
• Publications: 6 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 = 0.139 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.1038-20430G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.122 AC: 18291 AN: 150432 Hom.: 1149 Cov.: 31

Gnomad AFR AF: 0.115

Gnomad AMI AF: 0.206

Gnomad AMR AF: 0.0962

Gnomad ASJ AF: 0.219

Gnomad EAS AF: 0.148

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.0667

Gnomad MID AF: 0.0994

Gnomad NFE AF: 0.131

Gnomad OTH AF: 0.127

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

GnomAD4 genome AF: 0.121 AC: 18277 AN: 150532 Hom.: 1149 Cov.: 31 AF XY: 0.119 AC XY: 8743 AN XY: 73484

African (AFR) AF: 0.115 AC: 4743 AN: 41168

American (AMR) AF: 0.0960 AC: 1451 AN: 15118

Ashkenazi Jewish (ASJ) AF: 0.219 AC: 758 AN: 3462

East Asian (EAS) AF: 0.148 AC: 757 AN: 5132

South Asian (SAS) AF: 0.120 AC: 575 AN: 4778

European-Finnish (FIN) AF: 0.0667 AC: 676 AN: 10140

Middle Eastern (MID) AF: 0.0931 AC: 27 AN: 290

European-Non Finnish (NFE) AF: 0.131 AC: 8840 AN: 67446

Other (OTH) AF: 0.126 AC: 262 AN: 2086

Alfa AF: 0.129 Hom.: 1628

Bravo AF: 0.123

Asia WGS AF: 0.148 AC: 512 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.55
DANN	Benign	0.68
PhyloP100		-0.43

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: rs2050689;

hg19: chr6-78934100;