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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377865	XR_002956359.2	n.135-12412T>C		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000230309	ENST00000715178.1	n.1038-12412T>C		intron_variant	Intron 6 of 14

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 v4.3

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

Other links and lift over

dbSNP: rs9443543; hg19: chr6-78926082; COSMIC: COSV70045888;