rs12001727

Variant names:

• chr9-82785759-C-T
• rs12001727
• ENST00000792604.1:n.355-41315G>A

Variant summary

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

The ENST00000792604.1(ENSG00000303186):​n.355-41315G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.176 in 152,094 control chromosomes in the GnomAD database, including 2,858 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 0.18 (2858 hom., cov: 32)
• Consequence: ENSG00000303186 ENST00000792604.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.602
• Publications: 1 publications found

Genes affected

ENSG00000303186 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.396 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000303186	ENST00000792604.1	n.355-41315G>A		intron_variant	Intron 4 of 4
ENSG00000303186	ENST00000792605.1	n.202-3377G>A		intron_variant	Intron 2 of 3
ENSG00000303186	ENST00000792606.1	n.164-41315G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.176 AC: 26793 AN: 151974 Hom.: 2849 Cov.: 32

Gnomad AFR AF: 0.0742

Gnomad AMI AF: 0.161

Gnomad AMR AF: 0.208

Gnomad ASJ AF: 0.160

Gnomad EAS AF: 0.409

Gnomad SAS AF: 0.277

Gnomad FIN AF: 0.226

Gnomad MID AF: 0.182

Gnomad NFE AF: 0.199

Gnomad OTH AF: 0.207

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

GnomAD4 genome AF: 0.176 AC: 26824 AN: 152094 Hom.: 2858 Cov.: 32 AF XY: 0.183 AC XY: 13616 AN XY: 74360

African (AFR) AF: 0.0742 AC: 3082 AN: 41520

American (AMR) AF: 0.209 AC: 3191 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.160 AC: 554 AN: 3462

East Asian (EAS) AF: 0.410 AC: 2116 AN: 5156

South Asian (SAS) AF: 0.277 AC: 1333 AN: 4814

European-Finnish (FIN) AF: 0.226 AC: 2387 AN: 10582

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.199 AC: 13514 AN: 67984

Other (OTH) AF: 0.212 AC: 447 AN: 2104

Alfa AF: 0.194 Hom.: 1415

Bravo AF: 0.164

Asia WGS AF: 0.343 AC: 1194 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.3
DANN	Benign	0.60
PhyloP100		-0.60

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs12001727; hg19: chr9-85400674;