10-20573472-C-T

Variant names:

• chr10-20573472-C-T
• rs11012167
• ENST00000785943.1:n.368-32843C>T

Variant summary

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

The ENST00000785943.1(ENSG00000302338):​n.368-32843C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0385 in 152,224 control chromosomes in the GnomAD database, including 131 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 0.038 (131 hom., cov: 32)
• Consequence: ENSG00000302338 ENST00000785943.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.875
• Publications: 2 publications found

Genes affected

ENSG00000302338 (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 (AFR) allele frequency at 95% confidence interval = 0.0644 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
ENSG00000302338	ENST00000785943.1	n.368-32843C>T		intron_variant	Intron 2 of 5
ENSG00000302338	ENST00000785944.1	n.281-32843C>T		intron_variant	Intron 2 of 3
ENSG00000302338	ENST00000785945.1	n.215-32843C>T		intron_variant	Intron 2 of 4
ENSG00000302338	ENST00000785947.1	n.124-32885C>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.0385 AC: 5849 AN: 152106 Hom.: 130 Cov.: 32

Gnomad AFR AF: 0.0665

Gnomad AMI AF: 0.00768

Gnomad AMR AF: 0.0269

Gnomad ASJ AF: 0.0141

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0112

Gnomad FIN AF: 0.0428

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0301

Gnomad OTH AF: 0.0306

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

GnomAD4 genome AF: 0.0385 AC: 5855 AN: 152224 Hom.: 131 Cov.: 32 AF XY: 0.0380 AC XY: 2828 AN XY: 74430

African (AFR) AF: 0.0665 AC: 2762 AN: 41542

American (AMR) AF: 0.0269 AC: 411 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0141 AC: 49 AN: 3472

East Asian (EAS) AF: 0.000579 AC: 3 AN: 5182

South Asian (SAS) AF: 0.0110 AC: 53 AN: 4816

European-Finnish (FIN) AF: 0.0428 AC: 454 AN: 10596

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0301 AC: 2044 AN: 68008

Other (OTH) AF: 0.0307 AC: 65 AN: 2114

Alfa AF: 0.0267 Hom.: 26

Bravo AF: 0.0381

Asia WGS AF: 0.0130 AC: 46 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	9.0
DANN	Benign	0.54
PhyloP100		0.88

Splicing

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

Other links and lift over

dbSNP: rs11012167; hg19: chr10-20862401;