rs12634193

Variant names:

• chr3-171462896-T-C
• rs12634193
• ENST00000467896.3:n.871+1496T>C

Variant summary

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

The ENST00000467896.3(ENSG00000240497):​n.871+1496T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.773 in 152,136 control chromosomes in the GnomAD database, including 45,632 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 0.77 (45632 hom., cov: 33)
• Consequence: ENSG00000240497 ENST00000467896.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.41
• Publications: 6 publications found

Genes affected

ENSG00000240497 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.835 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000467896.3. 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
	LOC102724479	NR_189065.1		n.458+1539T>C		intron	N/A
	LOC102724479	NR_189066.1		n.458+1539T>C		intron	N/A
	LOC102724479	NR_189067.1		n.316+1681T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000240497	ENST00000467896.3	TSL:2	n.871+1496T>C		intron	N/A
	ENSG00000240497	ENST00000657847.2		n.162+3505T>C		intron	N/A
	ENSG00000240497	ENST00000665680.1		n.84+2604T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.773 AC: 117554 AN: 152018 Hom.: 45585 Cov.: 33

Gnomad AFR AF: 0.842

Gnomad AMI AF: 0.669

Gnomad AMR AF: 0.746

Gnomad ASJ AF: 0.796

Gnomad EAS AF: 0.758

Gnomad SAS AF: 0.711

Gnomad FIN AF: 0.753

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.747

Gnomad OTH AF: 0.769

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

GnomAD4 genome AF: 0.773 AC: 117664 AN: 152136 Hom.: 45632 Cov.: 33 AF XY: 0.771 AC XY: 57377 AN XY: 74394

African (AFR) AF: 0.842 AC: 34939 AN: 41490

American (AMR) AF: 0.746 AC: 11407 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.796 AC: 2764 AN: 3472

East Asian (EAS) AF: 0.758 AC: 3929 AN: 5186

South Asian (SAS) AF: 0.712 AC: 3432 AN: 4822

European-Finnish (FIN) AF: 0.753 AC: 7963 AN: 10574

Middle Eastern (MID) AF: 0.752 AC: 221 AN: 294

European-Non Finnish (NFE) AF: 0.747 AC: 50776 AN: 67992

Other (OTH) AF: 0.769 AC: 1624 AN: 2112

Alfa AF: 0.752 Hom.: 66536

Bravo AF: 0.780

Asia WGS AF: 0.748 AC: 2599 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.067
DANN	Benign	0.43
PhyloP100		-1.4

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: rs12634193;

hg19: chr3-171180685;