rs10512084

chr9-79208451-A-Cchr9-79208451-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007061599.1(LOC124902186):n.312A>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0141 in 152,296 control chromosomes in the GnomAD database, including 72 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 0.014 (72 hom., cov: 32)
• Consequence: LOC124902186 XR_007061599.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.274

Genes affected

LOC124902186 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.109 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124902186	XR_007061599.1	n.312A>C		non_coding_transcript_exon_variant	2/2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0141 AC: 2140 AN: 152178 Hom.: 71 Cov.: 32

Gnomad AFR AF: 0.00162

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.0251

Gnomad ASJ AF: 0.0118

Gnomad EAS AF: 0.118

Gnomad SAS AF: 0.100

Gnomad FIN AF: 0.000282

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.00750

Gnomad OTH AF: 0.0124

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

GnomAD4 genome AF: 0.0141 AC: 2142 AN: 152296 Hom.: 72 Cov.: 32 AF XY: 0.0166 AC XY: 1235 AN XY: 74470

Gnomad4 AFR AF: 0.00161

Gnomad4 AMR AF: 0.0252

Gnomad4 ASJ AF: 0.0118

Gnomad4 EAS AF: 0.117

Gnomad4 SAS AF: 0.101

Gnomad4 FIN AF: 0.000282

Gnomad4 NFE AF: 0.00750

Gnomad4 OTH AF: 0.0123

Alfa AF: 0.00951 Hom.: 3

Bravo AF: 0.0139

Asia WGS AF: 0.102 AC: 353 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	2.1
Dann	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10512084; hg19: chr9-81823366;