chr6-78224383-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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377865	XR_002956359.2	n.135-20430G>A		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000230309	ENST00000715178.1	n.1038-20430G>A		intron_variant	Intron 6 of 14

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 v4.3

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

Other links and lift over

dbSNP: rs2050689; hg19: chr6-78934100;