ENST00000685138.3:n.272+36267T>C

Variant names:

• chr20-41679187-A-G
• rs12480143
• ENST00000685138.3:n.272+36267T>C

Variant summary

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

The ENST00000685138.3(ENSG00000288843):​n.272+36267T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.3 in 151,746 control chromosomes in the GnomAD database, including 7,088 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 0.30 (7088 hom., cov: 31)
• Consequence: ENSG00000288843 ENST00000685138.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.774
• Publications: 3 publications found

Genes affected

ENSG00000288843 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.454 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
ENSG00000288843	ENST00000685138.3	n.272+36267T>C		intron_variant	Intron 1 of 1
ENSG00000288843	ENST00000686898.2	n.273-28679T>C		intron_variant	Intron 1 of 1
ENSG00000288843	ENST00000691734.2	n.403+27321T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.300 AC: 45467 AN: 151628 Hom.: 7068 Cov.: 31

Gnomad AFR AF: 0.344

Gnomad AMI AF: 0.225

Gnomad AMR AF: 0.322

Gnomad ASJ AF: 0.194

Gnomad EAS AF: 0.249

Gnomad SAS AF: 0.470

Gnomad FIN AF: 0.273

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.272

Gnomad OTH AF: 0.270

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

GnomAD4 genome AF: 0.300 AC: 45527 AN: 151746 Hom.: 7088 Cov.: 31 AF XY: 0.303 AC XY: 22473 AN XY: 74182

African (AFR) AF: 0.344 AC: 14257 AN: 41398

American (AMR) AF: 0.323 AC: 4924 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.194 AC: 672 AN: 3468

East Asian (EAS) AF: 0.249 AC: 1290 AN: 5174

South Asian (SAS) AF: 0.470 AC: 2263 AN: 4818

European-Finnish (FIN) AF: 0.273 AC: 2838 AN: 10414

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.272 AC: 18452 AN: 67910

Other (OTH) AF: 0.267 AC: 561 AN: 2098

Alfa AF: 0.298 Hom.: 1001

Bravo AF: 0.302

Asia WGS AF: 0.390 AC: 1356 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.45
PhyloP100		-0.77

Splicing

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

Other links and lift over

dbSNP: rs12480143; hg19: chr20-40307826;