rs9451437

chr6-90500167-A-C

Variant summary

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

The XR_007059678.1(LOC124901362):n.1114T>G 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 0.294 in 152,060 control chromosomes in the GnomAD database, including 7,495 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 0.29 (7495 hom., cov: 33)
• Consequence: LOC124901362 XR_007059678.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.486

Genes affected

LOC124901362 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.442 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124901362	XR_007059678.1	n.1114T>G		non_coding_transcript_exon_variant	1/2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.294 AC: 44615 AN: 151942 Hom.: 7486 Cov.: 33

Gnomad AFR AF: 0.448

Gnomad AMI AF: 0.301

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.375

Gnomad EAS AF: 0.0374

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.182

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.262

Gnomad OTH AF: 0.286

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

GnomAD4 genome AF: 0.294 AC: 44659 AN: 152060 Hom.: 7495 Cov.: 33 AF XY: 0.286 AC XY: 21263 AN XY: 74344

Gnomad4 AFR AF: 0.447

Gnomad4 AMR AF: 0.213

Gnomad4 ASJ AF: 0.375

Gnomad4 EAS AF: 0.0375

Gnomad4 SAS AF: 0.140

Gnomad4 FIN AF: 0.182

Gnomad4 NFE AF: 0.262

Gnomad4 OTH AF: 0.287

Alfa AF: 0.272 Hom.: 775

Bravo AF: 0.301

Asia WGS AF: 0.146 AC: 510 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	2.6
Dann	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9451437; hg19: chr6-91209886; COSMIC: COSV60243818;