rs12596341

Variant names:

• chr16-85933434-C-A
• rs12596341
• ENST00000645383.1:n.393+1160C>A

Variant summary

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

The ENST00000645383.1(ENSG00000285163):​n.393+1160C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0802 in 152,186 control chromosomes in the GnomAD database, including 672 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 0.080 (672 hom., cov: 31)
• Consequence: ENSG00000285163 ENST00000645383.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.776
• Publications: 1 publications found

Genes affected

ENSG00000285163 (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 (EAS) allele frequency at 95% confidence interval = 0.164 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000645383.1. 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
	ENSG00000285163	ENST00000645383.1		n.393+1160C>A		intron	N/A
	ENSG00000285163	ENST00000646214.1		n.77+8374C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0802 AC: 12202 AN: 152068 Hom.: 669 Cov.: 31

Gnomad AFR AF: 0.0203

Gnomad AMI AF: 0.222

Gnomad AMR AF: 0.0787

Gnomad ASJ AF: 0.158

Gnomad EAS AF: 0.174

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.0625

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.0952

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

GnomAD4 genome AF: 0.0802 AC: 12201 AN: 152186 Hom.: 672 Cov.: 31 AF XY: 0.0789 AC XY: 5867 AN XY: 74400

African (AFR) AF: 0.0202 AC: 839 AN: 41540

American (AMR) AF: 0.0785 AC: 1201 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.158 AC: 549 AN: 3470

East Asian (EAS) AF: 0.174 AC: 894 AN: 5148

South Asian (SAS) AF: 0.101 AC: 485 AN: 4808

European-Finnish (FIN) AF: 0.0625 AC: 663 AN: 10612

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.105 AC: 7130 AN: 67996

Other (OTH) AF: 0.0985 AC: 208 AN: 2112

Alfa AF: 0.0670 Hom.: 212

Bravo AF: 0.0791

Asia WGS AF: 0.118 AC: 410 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	2.1
DANN	Benign	0.33
PhyloP100		0.78

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: rs12596341;

hg19: chr16-85967040;