rs11787683

Variant names:

• chr9-29407112-G-T
• rs11787683
• ENST00000775037.1:n.254+43277C>A

Variant summary

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

The ENST00000775037.1(ENSG00000300910):​n.254+43277C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0451 in 140,298 control chromosomes in the GnomAD database, including 174 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 0.045 (174 hom., cov: 31)
• Consequence: ENSG00000300910 ENST00000775037.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.321
• Publications: 0 publications found

Genes affected

ENSG00000300910 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0897 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000775037.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000300910	ENST00000775037.1		n.254+43277C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0450 AC: 6303 AN: 140180 Hom.: 170 Cov.: 31

Gnomad AFR AF: 0.0609

Gnomad AMI AF: 0.151

Gnomad AMR AF: 0.0381

Gnomad ASJ AF: 0.0264

Gnomad EAS AF: 0.0974

Gnomad SAS AF: 0.0304

Gnomad FIN AF: 0.0253

Gnomad MID AF: 0.0367

Gnomad NFE AF: 0.0362

Gnomad OTH AF: 0.0410

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

GnomAD4 genome AF: 0.0451 AC: 6331 AN: 140298 Hom.: 174 Cov.: 31 AF XY: 0.0449 AC XY: 3049 AN XY: 67908

African (AFR) AF: 0.0613 AC: 2415 AN: 39378

American (AMR) AF: 0.0382 AC: 493 AN: 12906

Ashkenazi Jewish (ASJ) AF: 0.0264 AC: 87 AN: 3294

East Asian (EAS) AF: 0.0971 AC: 450 AN: 4636

South Asian (SAS) AF: 0.0309 AC: 129 AN: 4176

European-Finnish (FIN) AF: 0.0253 AC: 231 AN: 9146

Middle Eastern (MID) AF: 0.0426 AC: 12 AN: 282

European-Non Finnish (NFE) AF: 0.0362 AC: 2303 AN: 63692

Other (OTH) AF: 0.0406 AC: 77 AN: 1898

Alfa AF: 0.0384 Hom.: 12

Bravo AF: 0.0454

Asia WGS AF: 0.0520 AC: 183 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.3
DANN	Benign	0.65
PhyloP100		0.32

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs11787683;

hg19: chr9-29407110;

COSMIC: COSV69456961;