rs6782299

Variant names:

• chr3-180832914-G-T
• rs6782299
• ENST00000485055.5:n.250+14593C>A

Variant summary

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

The ENST00000485055.5(ENSG00000285336):​n.250+14593C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.802 in 152,190 control chromosomes in the GnomAD database, including 49,579 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 (49579 hom., cov: 33)
• Consequence: ENSG00000285336 ENST00000485055.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.995
• Publications: 23 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.941 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.250+14593C>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285336	ENST00000485055.5	TSL:1	n.250+14593C>A		intron	N/A
	ENSG00000145075	ENST00000471307.6	TSL:3	n.252+14593C>A		intron	N/A
	ENSG00000285336	ENST00000495817.1	TSL:3	n.206+37886C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.802 AC: 121905 AN: 152074 Hom.: 49528 Cov.: 33

Gnomad AFR AF: 0.949

Gnomad AMI AF: 0.704

Gnomad AMR AF: 0.778

Gnomad ASJ AF: 0.688

Gnomad EAS AF: 0.854

Gnomad SAS AF: 0.721

Gnomad FIN AF: 0.784

Gnomad MID AF: 0.742

Gnomad NFE AF: 0.730

Gnomad OTH AF: 0.762

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

GnomAD4 genome AF: 0.802 AC: 122009 AN: 152190 Hom.: 49579 Cov.: 33 AF XY: 0.803 AC XY: 59740 AN XY: 74396

African (AFR) AF: 0.949 AC: 39432 AN: 41552

American (AMR) AF: 0.778 AC: 11905 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.688 AC: 2387 AN: 3472

East Asian (EAS) AF: 0.854 AC: 4422 AN: 5178

South Asian (SAS) AF: 0.722 AC: 3475 AN: 4816

European-Finnish (FIN) AF: 0.784 AC: 8303 AN: 10584

Middle Eastern (MID) AF: 0.733 AC: 214 AN: 292

European-Non Finnish (NFE) AF: 0.730 AC: 49633 AN: 67982

Other (OTH) AF: 0.757 AC: 1596 AN: 2108

Alfa AF: 0.760 Hom.: 80651

Bravo AF: 0.809

Asia WGS AF: 0.765 AC: 2664 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.21
DANN	Benign	0.77
PhyloP100		-0.99

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: rs6782299;

hg19: chr3-180550702;