ENST00000428533.5:n.138+49971C>A

Variant names:

• chr7-11247415-C-A
• rs2353803
• ENST00000428533.5:n.138+49971C>A

Variant summary

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

The ENST00000428533.5(ENSG00000230333):​n.138+49971C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0939 in 152,002 control chromosomes in the GnomAD database, including 780 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 0.094 (780 hom., cov: 32)
• Consequence: ENSG00000230333 ENST00000428533.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.544
• Publications: 2 publications found

Genes affected

ENSG00000230333 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.12 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000428533.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000230333	ENST00000428533.5	TSL:5	n.138+49971C>A		intron	N/A
	ENSG00000230333	ENST00000428967.5	TSL:4	n.415-878C>A		intron	N/A
	ENSG00000230333	ENST00000441110.5	TSL:3	n.546+2936C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0940 AC: 14272 AN: 151884 Hom.: 776 Cov.: 32

Gnomad AFR AF: 0.0594

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.0813

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.000579

Gnomad SAS AF: 0.0875

Gnomad FIN AF: 0.0844

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.104

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

GnomAD4 genome AF: 0.0939 AC: 14280 AN: 152002 Hom.: 780 Cov.: 32 AF XY: 0.0916 AC XY: 6810 AN XY: 74314

African (AFR) AF: 0.0596 AC: 2475 AN: 41504

American (AMR) AF: 0.0811 AC: 1238 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.175 AC: 608 AN: 3466

East Asian (EAS) AF: 0.000580 AC: 3 AN: 5168

South Asian (SAS) AF: 0.0875 AC: 421 AN: 4810

European-Finnish (FIN) AF: 0.0844 AC: 889 AN: 10538

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.122 AC: 8283 AN: 67940

Other (OTH) AF: 0.103 AC: 217 AN: 2108

Alfa AF: 0.112 Hom.: 121

Bravo AF: 0.0933

Asia WGS AF: 0.0390 AC: 137 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.0
DANN	Benign	0.71
PhyloP100		-0.54

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2353803; hg19: chr7-11287042;