rs2225614

Variant names:

• chr9-24111282-C-A
• rs2225614
• ENST00000850878.1:n.505+21968C>A

Your query was ambiguous. Multiple possible variants found:

• chr9-24111282-C-A
• chr9-24111282-C-G
• chr9-24111282-C-T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000850878.1(ENSG00000300787):​n.505+21968C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.201 in 152,120 control chromosomes in the GnomAD database, including 3,773 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 0.20 (3773 hom., cov: 32)
• Consequence: ENSG00000300787 ENST00000850878.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.156
• Publications: 8 publications found

Genes affected

ENSG00000300787 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.27).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.617 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+21968C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.201 AC: 30550 AN: 152002 Hom.: 3762 Cov.: 32

Gnomad AFR AF: 0.133

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.252

Gnomad ASJ AF: 0.273

Gnomad EAS AF: 0.635

Gnomad SAS AF: 0.245

Gnomad FIN AF: 0.178

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.195

Gnomad OTH AF: 0.210

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

GnomAD4 genome AF: 0.201 AC: 30575 AN: 152120 Hom.: 3773 Cov.: 32 AF XY: 0.205 AC XY: 15241 AN XY: 74366

African (AFR) AF: 0.133 AC: 5526 AN: 41496

American (AMR) AF: 0.253 AC: 3865 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.273 AC: 947 AN: 3470

East Asian (EAS) AF: 0.635 AC: 3270 AN: 5146

South Asian (SAS) AF: 0.246 AC: 1184 AN: 4816

European-Finnish (FIN) AF: 0.178 AC: 1888 AN: 10596

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.195 AC: 13284 AN: 68008

Other (OTH) AF: 0.211 AC: 447 AN: 2114

Alfa AF: 0.207 Hom.: 16409

Bravo AF: 0.206

Asia WGS AF: 0.390 AC: 1355 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.27
CADD	Benign	15
DANN	Benign	0.80
PhyloP100		0.16

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: rs2225614;

hg19: chr9-24111280;

COSMIC: COSV62761449;