ENST00000685138.2:n.272+36267T>C

Variant names:

• chr20-41679187-A-G
• rs12480143
• ENST00000685138.2:n.272+36267T>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000685138.2(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 ENST00000685138.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.774

Genes affected

ENSG00000288843 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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	ENST00000685138.2	n.272+36267T>C		intron_variant	Intron 1 of 1
ENSG00000288843	ENST00000686898.1	n.238-28679T>C		intron_variant	Intron 1 of 1
ENSG00000288843	ENST00000691734.1	n.355+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

Gnomad4 AFR AF: 0.344

Gnomad4 AMR AF: 0.323

Gnomad4 ASJ AF: 0.194

Gnomad4 EAS AF: 0.249

Gnomad4 SAS AF: 0.470

Gnomad4 FIN AF: 0.273

Gnomad4 NFE AF: 0.272

Gnomad4 OTH AF: 0.267

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12480143; hg19: chr20-40307826;