rs725318

Variant names:

• chr3-178123979-A-G
• rs725318
• ENST00000651726.1:n.234+48237T>C

Your query was ambiguous. Multiple possible variants found:

• chr3-178123979-A-G
• chr3-178123979-A-T

Variant summary

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

The ENST00000651726.1(ENSG00000286003):​n.234+48237T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.435 in 152,010 control chromosomes in the GnomAD database, including 15,081 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 0.44 (15081 hom., cov: 32)
• Consequence: ENSG00000286003 ENST00000651726.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.150
• Publications: 4 publications found

Genes affected

ENSG00000286003 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.72 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000651726.1. 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
	ENSG00000286003	ENST00000651726.1		n.234+48237T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.436 AC: 66154 AN: 151894 Hom.: 15072 Cov.: 32

Gnomad AFR AF: 0.316

Gnomad AMI AF: 0.370

Gnomad AMR AF: 0.517

Gnomad ASJ AF: 0.572

Gnomad EAS AF: 0.739

Gnomad SAS AF: 0.481

Gnomad FIN AF: 0.462

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.453

Gnomad OTH AF: 0.441

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

GnomAD4 genome AF: 0.435 AC: 66190 AN: 152010 Hom.: 15081 Cov.: 32 AF XY: 0.441 AC XY: 32738 AN XY: 74318

African (AFR) AF: 0.316 AC: 13091 AN: 41472

American (AMR) AF: 0.518 AC: 7912 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.572 AC: 1981 AN: 3464

East Asian (EAS) AF: 0.739 AC: 3817 AN: 5162

South Asian (SAS) AF: 0.481 AC: 2318 AN: 4820

European-Finnish (FIN) AF: 0.462 AC: 4880 AN: 10552

Middle Eastern (MID) AF: 0.459 AC: 134 AN: 292

European-Non Finnish (NFE) AF: 0.453 AC: 30781 AN: 67946

Other (OTH) AF: 0.445 AC: 939 AN: 2112

Alfa AF: 0.418 Hom.: 2216

Bravo AF: 0.435

Asia WGS AF: 0.594 AC: 2064 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.5
DANN	Benign	0.77
PhyloP100		0.15

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: rs725318;

hg19: chr3-177841767;