rs9397436

chr6-151630867-A-G

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

LOC124901435 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124901435	XR_007059816.1	n.3759A>G		non_coding_transcript_exon_variant	2/2

Ensembl

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

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

Gnomad4 AFR AF: 0.0786

Gnomad4 AMR AF: 0.0630

Gnomad4 ASJ AF: 0.0830

Gnomad4 EAS AF: 0.302

Gnomad4 SAS AF: 0.0829

Gnomad4 FIN AF: 0.0259

Gnomad4 NFE AF: 0.0696

Gnomad4 OTH AF: 0.0917

Alfa AF: 0.0704 Hom.: 125

Bravo AF: 0.0811

Asia WGS AF: 0.175 AC: 607 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
Cadd	Benign	1.9
Dann	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9397436; hg19: chr6-151952002;