chr11-9573280-G-A

Variant names:

• chr11-9573280-G-A
• rs3763869
• ENST00000827706.1:n.120C>T

Variant summary

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

The ENST00000827706.1(ENSG00000307659):​n.120C>T 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 0.58 in 152,168 control chromosomes in the GnomAD database, including 26,019 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 (26019 hom., cov: 34)
• Consequence: ENSG00000307659 ENST00000827706.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00400
• Publications: 9 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=-0.67).
• 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.120C>T		non_coding_transcript_exon_variant	Exon 1 of 1
ENSG00000307677	ENST00000827821.1	n.405G>A		non_coding_transcript_exon_variant	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.580 AC: 88195 AN: 152050 Hom.: 25985 Cov.: 34

Gnomad AFR AF: 0.518

Gnomad AMI AF: 0.605

Gnomad AMR AF: 0.525

Gnomad ASJ AF: 0.578

Gnomad EAS AF: 0.385

Gnomad SAS AF: 0.612

Gnomad FIN AF: 0.657

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.633

Gnomad OTH AF: 0.533

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

GnomAD4 genome AF: 0.580 AC: 88285 AN: 152168 Hom.: 26019 Cov.: 34 AF XY: 0.581 AC XY: 43233 AN XY: 74418

African (AFR) AF: 0.518 AC: 21511 AN: 41520

American (AMR) AF: 0.525 AC: 8035 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.578 AC: 2007 AN: 3472

East Asian (EAS) AF: 0.385 AC: 1993 AN: 5172

South Asian (SAS) AF: 0.613 AC: 2962 AN: 4834

European-Finnish (FIN) AF: 0.657 AC: 6968 AN: 10602

Middle Eastern (MID) AF: 0.466 AC: 137 AN: 294

European-Non Finnish (NFE) AF: 0.633 AC: 43004 AN: 67962

Other (OTH) AF: 0.530 AC: 1119 AN: 2110

Alfa AF: 0.605 Hom.: 27944

Bravo AF: 0.560

Asia WGS AF: 0.496 AC: 1726 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	7.5
DANN	Benign	0.89
PhyloP100		0.0040
PromoterAI		0.31	Neutral

Splicing

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

Other links and lift over

dbSNP: rs3763869; hg19: chr11-9594827;