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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124902327	XR_007061897.1	n.96-35154C>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000300787	ENST00000850878.1	n.505+21968C>A		intron_variant	Intron 4 of 4

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 v4.3

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

Other links and lift over

dbSNP: rs2225614; hg19: chr9-24111280; COSMIC: COSV62761449;