rs4246856

Variant names:

• chr9-24092074-C-G
• rs4246856
• ENST00000850878.1:n.505+2760C>G

Variant summary

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

The ENST00000850878.1(ENSG00000300787):​n.505+2760C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.21 in 151,952 control chromosomes in the GnomAD database, including 4,178 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 0.21 (4178 hom., cov: 32)
• Consequence: ENSG00000300787 ENST00000850878.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.979
• Publications: 7 publications found

Genes affected

ENSG00000300787 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.63 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000850878.1. 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
	ENSG00000300787	ENST00000850878.1		n.505+2760C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.210 AC: 31815 AN: 151834 Hom.: 4165 Cov.: 32

Gnomad AFR AF: 0.128

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.287

Gnomad EAS AF: 0.648

Gnomad SAS AF: 0.246

Gnomad FIN AF: 0.181

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.203

Gnomad OTH AF: 0.224

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

GnomAD4 genome AF: 0.210 AC: 31841 AN: 151952 Hom.: 4178 Cov.: 32 AF XY: 0.213 AC XY: 15818 AN XY: 74254

African (AFR) AF: 0.128 AC: 5291 AN: 41492

American (AMR) AF: 0.309 AC: 4702 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.287 AC: 998 AN: 3472

East Asian (EAS) AF: 0.648 AC: 3328 AN: 5136

South Asian (SAS) AF: 0.247 AC: 1188 AN: 4816

European-Finnish (FIN) AF: 0.181 AC: 1912 AN: 10576

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.203 AC: 13779 AN: 67914

Other (OTH) AF: 0.226 AC: 477 AN: 2110

Alfa AF: 0.223 Hom.: 2452

Bravo AF: 0.219

Asia WGS AF: 0.397 AC: 1379 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.16
DANN	Benign	0.31
PhyloP100		-0.98

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: rs4246856;

hg19: chr9-24092072;