rs9397437

Variant names:

• chr6-151631197-G-A
• rs9397437
• XR_007059816.1:n.4089G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 33 publications found

Genes affected

LOC124901435 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.0478 AC: 1972 AN: 41262

American (AMR) AF: 0.0617 AC: 940 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.0833 AC: 289 AN: 3470

East Asian (EAS) AF: 0.302 AC: 1548 AN: 5124

South Asian (SAS) AF: 0.0828 AC: 398 AN: 4808

European-Finnish (FIN) AF: 0.0262 AC: 273 AN: 10416

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.0696 AC: 4727 AN: 67916

Other (OTH) AF: 0.0858 AC: 180 AN: 2098

Alfa AF: 0.0710 Hom.: 851

Bravo AF: 0.0716

Asia WGS AF: 0.170 AC: 590 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.2
DANN	Benign	0.60
PhyloP100		0.47

Splicing

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

Other links and lift over

dbSNP: rs9397437; hg19: chr6-151952332;