11-9573341-G-C

Variant names:

• chr11-9573341-G-C
• rs3763868
• ENST00000827706.1:n.59C>G

Variant summary

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

The ENST00000827706.1(ENSG00000307659):​n.59C>G 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 0.582 in 152,118 control chromosomes in the GnomAD database, including 26,191 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 0.58 (26191 hom., cov: 34)
• Consequence: ENSG00000307659 ENST00000827706.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29
• Publications: 4 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=-0.76).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.628 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.59C>G		non_coding_transcript_exon_variant	Exon 1 of 1
ENSG00000307677	ENST00000827821.1	n.*41G>C		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.582 AC: 88470 AN: 151998 Hom.: 26164 Cov.: 34

Gnomad AFR AF: 0.523

Gnomad AMI AF: 0.607

Gnomad AMR AF: 0.526

Gnomad ASJ AF: 0.578

Gnomad EAS AF: 0.387

Gnomad SAS AF: 0.612

Gnomad FIN AF: 0.657

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.633

Gnomad OTH AF: 0.536

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

GnomAD4 genome AF: 0.582 AC: 88550 AN: 152118 Hom.: 26191 Cov.: 34 AF XY: 0.583 AC XY: 43357 AN XY: 74366

African (AFR) AF: 0.523 AC: 21697 AN: 41486

American (AMR) AF: 0.526 AC: 8045 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.578 AC: 2005 AN: 3466

East Asian (EAS) AF: 0.387 AC: 1993 AN: 5146

South Asian (SAS) AF: 0.613 AC: 2960 AN: 4828

European-Finnish (FIN) AF: 0.657 AC: 6975 AN: 10612

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.633 AC: 43060 AN: 67978

Other (OTH) AF: 0.534 AC: 1126 AN: 2110

Alfa AF: 0.509 Hom.: 1583

Bravo AF: 0.562

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	1.6
DANN	Benign	0.37
PhyloP100		-1.3
PromoterAI		-0.039	Neutral

Splicing

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

Other links and lift over

dbSNP: rs3763868; hg19: chr11-9594888;