rs16910061

chr9-94552459-G-Achr9-94552459-G-C

Variant summary

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

The XR_007061674.1(LOC124902218):n.1227C>T 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 0.0511 in 152,250 control chromosomes in the GnomAD database, including 333 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 0.051 (333 hom., cov: 33)
• Consequence: LOC124902218 XR_007061674.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.204

Genes affected

LOC124902218 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.142 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124902218	XR_007061674.1	n.1227C>T		non_coding_transcript_exon_variant	2/2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0511 AC: 7772 AN: 152132 Hom.: 331 Cov.: 33

Gnomad AFR AF: 0.0873

Gnomad AMI AF: 0.0164

Gnomad AMR AF: 0.0837

Gnomad ASJ AF: 0.0179

Gnomad EAS AF: 0.150

Gnomad SAS AF: 0.0988

Gnomad FIN AF: 0.0123

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0194

Gnomad OTH AF: 0.0359

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

GnomAD4 genome AF: 0.0511 AC: 7787 AN: 152250 Hom.: 333 Cov.: 33 AF XY: 0.0532 AC XY: 3957 AN XY: 74436

Gnomad4 AFR AF: 0.0872

Gnomad4 AMR AF: 0.0840

Gnomad4 ASJ AF: 0.0179

Gnomad4 EAS AF: 0.151

Gnomad4 SAS AF: 0.0986

Gnomad4 FIN AF: 0.0123

Gnomad4 NFE AF: 0.0194

Gnomad4 OTH AF: 0.0369

Alfa AF: 0.0315 Hom.: 153

Bravo AF: 0.0591

Asia WGS AF: 0.113 AC: 395 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	0.90
Dann	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16910061; hg19: chr9-97314741;