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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901435	XR_007059816.1	n.4089G>A		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

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 v4.3

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;