rs2225614

Positions:

• chr9-24111282-C-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The XR_007061897.1(LOC124902327):​n.96-35154C>A variant causes a intron, non coding transcript 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: LOC124902327 XR_007061897.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.156

Genes affected

LOC124902327 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC124902327	XR_007061897.1	n.96-35154C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.133

Gnomad4 AMR AF: 0.253

Gnomad4 ASJ AF: 0.273

Gnomad4 EAS AF: 0.635

Gnomad4 SAS AF: 0.246

Gnomad4 FIN AF: 0.178

Gnomad4 NFE AF: 0.195

Gnomad4 OTH AF: 0.211

Alfa AF: 0.210 Hom.: 8484

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

Splicing

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

Publications

LitVar

Other links and lift over

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