rs9443543

Variant names:

• chr6-78216365-A-G
• rs9443543
• ENST00000715178.1:n.1038-12412T>C

Variant summary

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

The ENST00000715178.1(ENSG00000230309):​n.1038-12412T>C 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 152,064 control chromosomes in the GnomAD database, including 1,151 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 (1151 hom., cov: 32)
• Consequence: ENSG00000230309 ENST00000715178.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0900
• 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.134 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.1038-12412T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.121 AC: 18397 AN: 151946 Hom.: 1151 Cov.: 32

Gnomad AFR AF: 0.115

Gnomad AMI AF: 0.205

Gnomad AMR AF: 0.0957

Gnomad ASJ AF: 0.218

Gnomad EAS AF: 0.143

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.0651

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.131

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.121 AC: 18385 AN: 152064 Hom.: 1151 Cov.: 32 AF XY: 0.118 AC XY: 8780 AN XY: 74330

African (AFR) AF: 0.115 AC: 4762 AN: 41516

American (AMR) AF: 0.0955 AC: 1456 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.218 AC: 757 AN: 3466

East Asian (EAS) AF: 0.142 AC: 734 AN: 5154

South Asian (SAS) AF: 0.120 AC: 578 AN: 4822

European-Finnish (FIN) AF: 0.0651 AC: 691 AN: 10616

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.131 AC: 8933 AN: 67934

Other (OTH) AF: 0.124 AC: 261 AN: 2104

Alfa AF: 0.131 Hom.: 712

Bravo AF: 0.123

Asia WGS AF: 0.147 AC: 511 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	7.8
DANN	Benign	0.77
PhyloP100		0.090

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: rs9443543;

hg19: chr6-78926082;

COSMIC: COSV70045888;