11-9573143-T-G

Variant names:

• chr11-9573143-T-G
• rs6486433
• ENST00000827706.1:n.257A>C

Variant summary

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

The ENST00000827706.1(ENSG00000307659):​n.257A>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.617 in 152,096 control chromosomes in the GnomAD database, including 29,264 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 0.62 (29264 hom., cov: 33)
• Consequence: ENSG00000307659 ENST00000827706.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0250
• Publications: 3 publications found

Genes affected

ENSG00000307659 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.64 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
ENSG00000307659	ENST00000827706.1	n.257A>C		non_coding_transcript_exon_variant	Exon 1 of 1
ENSG00000307677	ENST00000827821.1	n.268T>G		non_coding_transcript_exon_variant	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.617 AC: 93789 AN: 151978 Hom.: 29222 Cov.: 33

Gnomad AFR AF: 0.646

Gnomad AMI AF: 0.606

Gnomad AMR AF: 0.539

Gnomad ASJ AF: 0.578

Gnomad EAS AF: 0.386

Gnomad SAS AF: 0.614

Gnomad FIN AF: 0.658

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.633

Gnomad OTH AF: 0.563

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

GnomAD4 genome AF: 0.617 AC: 93888 AN: 152096 Hom.: 29264 Cov.: 33 AF XY: 0.617 AC XY: 45860 AN XY: 74356

African (AFR) AF: 0.647 AC: 26804 AN: 41452

American (AMR) AF: 0.539 AC: 8245 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.578 AC: 2007 AN: 3470

East Asian (EAS) AF: 0.386 AC: 1997 AN: 5172

South Asian (SAS) AF: 0.614 AC: 2962 AN: 4824

European-Finnish (FIN) AF: 0.658 AC: 6969 AN: 10592

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.633 AC: 43030 AN: 67966

Other (OTH) AF: 0.560 AC: 1182 AN: 2112

Alfa AF: 0.607 Hom.: 8244

Bravo AF: 0.602

Asia WGS AF: 0.511 AC: 1778 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	1.7
DANN	Benign	0.41
PhyloP100		0.025

Splicing

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

Other links and lift over

dbSNP: rs6486433; hg19: chr11-9594690;