rs2383811

Variant names:

• chr9-29416255-G-A
• rs2383811
• ENST00000775037.1:n.254+34134C>T

Your query was ambiguous. Multiple possible variants found:

• chr9-29416255-G-A
• chr9-29416255-G-C

Variant summary

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

The ENST00000775037.1(ENSG00000300910):​n.254+34134C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.885 in 150,756 control chromosomes in the GnomAD database, including 59,086 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 0.88 (59086 hom., cov: 29)
• Consequence: ENSG00000300910 ENST00000775037.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.264
• Publications: 1 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 = 0.949 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+34134C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.885 AC: 133292 AN: 150636 Hom.: 59030 Cov.: 29

Gnomad AFR AF: 0.856

Gnomad AMI AF: 0.798

Gnomad AMR AF: 0.929

Gnomad ASJ AF: 0.893

Gnomad EAS AF: 0.972

Gnomad SAS AF: 0.854

Gnomad FIN AF: 0.927

Gnomad MID AF: 0.854

Gnomad NFE AF: 0.882

Gnomad OTH AF: 0.888

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

GnomAD4 genome AF: 0.885 AC: 133406 AN: 150756 Hom.: 59086 Cov.: 29 AF XY: 0.886 AC XY: 65248 AN XY: 73624

African (AFR) AF: 0.856 AC: 35278 AN: 41200

American (AMR) AF: 0.929 AC: 13990 AN: 15064

Ashkenazi Jewish (ASJ) AF: 0.893 AC: 3072 AN: 3440

East Asian (EAS) AF: 0.972 AC: 4959 AN: 5104

South Asian (SAS) AF: 0.854 AC: 4094 AN: 4796

European-Finnish (FIN) AF: 0.927 AC: 9820 AN: 10592

Middle Eastern (MID) AF: 0.854 AC: 251 AN: 294

European-Non Finnish (NFE) AF: 0.882 AC: 59353 AN: 67260

Other (OTH) AF: 0.889 AC: 1863 AN: 2096

Alfa AF: 0.878 Hom.: 29990

Bravo AF: 0.886

Asia WGS AF: 0.923 AC: 3210 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.0
DANN	Benign	0.61
PhyloP100		0.26

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: rs2383811;

hg19: chr9-29416253;