rs3934658

Variant names:

• chr12-121599194-A-C
• rs3934658
• ENST00000786201.1:n.180-3159T>G

Your query was ambiguous. Multiple possible variants found:

• chr12-121599194-A-C
• chr12-121599194-A-T

Variant summary

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

The ENST00000786201.1(ENSG00000302371):​n.180-3159T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.486 in 151,934 control chromosomes in the GnomAD database, including 18,847 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 0.49 (18847 hom., cov: 31)
• Consequence: ENSG00000302371 ENST00000786201.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.195
• Publications: 6 publications found

Genes affected

ENSG00000302371 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.643 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000786201.1. 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
	ENSG00000302371	ENST00000786201.1		n.180-3159T>G		intron	N/A
	ENSG00000302371	ENST00000786202.1		n.182-3159T>G		intron	N/A
	ENSG00000302371	ENST00000786203.1		n.180-3159T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.485 AC: 73669 AN: 151816 Hom.: 18788 Cov.: 31

Gnomad AFR AF: 0.648

Gnomad AMI AF: 0.402

Gnomad AMR AF: 0.441

Gnomad ASJ AF: 0.395

Gnomad EAS AF: 0.503

Gnomad SAS AF: 0.486

Gnomad FIN AF: 0.422

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.412

Gnomad OTH AF: 0.446

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

GnomAD4 genome AF: 0.486 AC: 73801 AN: 151934 Hom.: 18847 Cov.: 31 AF XY: 0.485 AC XY: 36017 AN XY: 74262

African (AFR) AF: 0.649 AC: 26875 AN: 41400

American (AMR) AF: 0.442 AC: 6731 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.395 AC: 1371 AN: 3470

East Asian (EAS) AF: 0.504 AC: 2599 AN: 5160

South Asian (SAS) AF: 0.486 AC: 2349 AN: 4830

European-Finnish (FIN) AF: 0.422 AC: 4452 AN: 10562

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.412 AC: 28010 AN: 67966

Other (OTH) AF: 0.447 AC: 941 AN: 2106

Alfa AF: 0.435 Hom.: 10698

Bravo AF: 0.494

Asia WGS AF: 0.520 AC: 1810 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.4
DANN	Benign	0.29
PhyloP100		-0.20

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: rs3934658;

hg19: chr12-122037099;