3-180815463-C-A

Variant names:

• chr3-180815463-C-A
• rs9838229
• ENST00000485055.5:n.251-4993G>T

Variant summary

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

The ENST00000485055.5(ENSG00000285336):​n.251-4993G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.798 in 152,190 control chromosomes in the GnomAD database, including 49,064 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 0.80 (49064 hom., cov: 33)
• Consequence: ENSG00000285336 ENST00000485055.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.584
• Publications: 7 publications found

Genes affected

ENSG00000285336 (HGNC:58949):

ENSG00000145075 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.929 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000485055.5. 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
	LOC101928882	NR_109986.1		n.251-4993G>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285336	ENST00000485055.5	TSL:1	n.251-4993G>T		intron	N/A
	ENSG00000145075	ENST00000471307.6	TSL:3	n.252+32044G>T		intron	N/A
	ENSG00000285336	ENST00000495817.1	TSL:3	n.207-33339G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.798 AC: 121338 AN: 152072 Hom.: 49020 Cov.: 33

Gnomad AFR AF: 0.937

Gnomad AMI AF: 0.704

Gnomad AMR AF: 0.776

Gnomad ASJ AF: 0.688

Gnomad EAS AF: 0.852

Gnomad SAS AF: 0.721

Gnomad FIN AF: 0.785

Gnomad MID AF: 0.741

Gnomad NFE AF: 0.730

Gnomad OTH AF: 0.758

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

GnomAD4 genome AF: 0.798 AC: 121436 AN: 152190 Hom.: 49064 Cov.: 33 AF XY: 0.799 AC XY: 59480 AN XY: 74414

African (AFR) AF: 0.937 AC: 38931 AN: 41536

American (AMR) AF: 0.776 AC: 11868 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.688 AC: 2385 AN: 3468

East Asian (EAS) AF: 0.853 AC: 4408 AN: 5170

South Asian (SAS) AF: 0.721 AC: 3473 AN: 4816

European-Finnish (FIN) AF: 0.785 AC: 8305 AN: 10586

Middle Eastern (MID) AF: 0.731 AC: 215 AN: 294

European-Non Finnish (NFE) AF: 0.730 AC: 49616 AN: 68008

Other (OTH) AF: 0.753 AC: 1594 AN: 2116

Alfa AF: 0.747 Hom.: 183171

Bravo AF: 0.805

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.53
DANN	Benign	0.31
PhyloP100		-0.58

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: rs9838229;

hg19: chr3-180533251;