rs9397437

Positions:

• chr6-151631197-G-A

Variant summary

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

The XR_007059816.1(LOC124901435):​n.4089G>A 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 0.0686 in 151,532 control chromosomes in the GnomAD database, including 548 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 0.069 (548 hom., cov: 32)
• Consequence: LOC124901435 XR_007059816.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.465

Genes affected

LOC124901435 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.29 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124901435	XR_007059816.1	n.4089G>A		non_coding_transcript_exon_variant	2/2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0687 AC: 10399 AN: 151414 Hom.: 548 Cov.: 32

Gnomad AFR AF: 0.0477

Gnomad AMI AF: 0.0374

Gnomad AMR AF: 0.0618

Gnomad ASJ AF: 0.0833

Gnomad EAS AF: 0.303

Gnomad SAS AF: 0.0825

Gnomad FIN AF: 0.0262

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.0696

Gnomad OTH AF: 0.0857

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

GnomAD4 genome AF: 0.0686 AC: 10399 AN: 151532 Hom.: 548 Cov.: 32 AF XY: 0.0678 AC XY: 5016 AN XY: 73990

Gnomad4 AFR AF: 0.0478

Gnomad4 AMR AF: 0.0617

Gnomad4 ASJ AF: 0.0833

Gnomad4 EAS AF: 0.302

Gnomad4 SAS AF: 0.0828

Gnomad4 FIN AF: 0.0262

Gnomad4 NFE AF: 0.0696

Gnomad4 OTH AF: 0.0858

Alfa AF: 0.0642 Hom.: 117

Bravo AF: 0.0716

Asia WGS AF: 0.170 AC: 590 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.2
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9397437; hg19: chr6-151952332;