rs9397436

Variant names:

• chr6-151630867-A-G
• rs9397436
• XR_007059816.1:n.3759A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007059816.1(LOC124901435):​n.3759A>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 0.0772 in 152,308 control chromosomes in the GnomAD database, including 635 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 0.077 (635 hom., cov: 33)
• Consequence: LOC124901435 XR_007059816.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0960
• Publications: 13 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=-0.71).
• 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: 0.0772 AC: 11747 AN: 152190 Hom.: 631 Cov.: 33

Gnomad AFR AF: 0.0784

Gnomad AMI AF: 0.0373

Gnomad AMR AF: 0.0631

Gnomad ASJ AF: 0.0830

Gnomad EAS AF: 0.303

Gnomad SAS AF: 0.0826

Gnomad FIN AF: 0.0259

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.0696

Gnomad OTH AF: 0.0917

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

GnomAD4 genome AF: 0.0772 AC: 11758 AN: 152308 Hom.: 635 Cov.: 33 AF XY: 0.0762 AC XY: 5672 AN XY: 74478

African (AFR) AF: 0.0786 AC: 3267 AN: 41562

American (AMR) AF: 0.0630 AC: 964 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0830 AC: 288 AN: 3468

East Asian (EAS) AF: 0.302 AC: 1565 AN: 5180

South Asian (SAS) AF: 0.0829 AC: 400 AN: 4826

European-Finnish (FIN) AF: 0.0259 AC: 275 AN: 10618

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

European-Non Finnish (NFE) AF: 0.0696 AC: 4733 AN: 68032

Other (OTH) AF: 0.0917 AC: 194 AN: 2116

Alfa AF: 0.0767 Hom.: 385

Bravo AF: 0.0811

Asia WGS AF: 0.175 AC: 607 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	1.9
DANN	Benign	0.70
PhyloP100		0.096

Splicing

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

Other links and lift over

dbSNP: rs9397436; hg19: chr6-151952002;