rs9397435

Variant names:

• chr6-151630085-A-G
• rs9397435
• XR_007059816.1:n.3408+103A>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.3408+103A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0787 in 152,302 control chromosomes in the GnomAD database, including 646 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (no stars).

• Frequency: Genomes: 𝑓 0.079 (646 hom., cov: 33)
• Consequence: LOC124901435 XR_007059816.1 intron
• Clinical Significance: Uncertain significance no assertion criteria provided U:1
• Conservation: PhyloP100: -1.70
• Publications: 34 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.289 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: 0.0787 AC: 11979 AN: 152184 Hom.: 642 Cov.: 33

Gnomad AFR AF: 0.0830

Gnomad AMI AF: 0.0373

Gnomad AMR AF: 0.0637

Gnomad ASJ AF: 0.0832

Gnomad EAS AF: 0.302

Gnomad SAS AF: 0.0835

Gnomad FIN AF: 0.0261

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.0700

Gnomad OTH AF: 0.0926

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

GnomAD4 genome AF: 0.0787 AC: 11989 AN: 152302 Hom.: 646 Cov.: 33 AF XY: 0.0776 AC XY: 5783 AN XY: 74484

African (AFR) AF: 0.0832 AC: 3458 AN: 41556

American (AMR) AF: 0.0636 AC: 974 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0832 AC: 289 AN: 3472

East Asian (EAS) AF: 0.302 AC: 1560 AN: 5172

South Asian (SAS) AF: 0.0837 AC: 404 AN: 4824

European-Finnish (FIN) AF: 0.0261 AC: 277 AN: 10624

Middle Eastern (MID) AF: 0.127 AC: 37 AN: 292

European-Non Finnish (NFE) AF: 0.0700 AC: 4760 AN: 68030

Other (OTH) AF: 0.0926 AC: 196 AN: 2116

Alfa AF: 0.0698 Hom.: 223

Bravo AF: 0.0827

Asia WGS AF: 0.176 AC: 609 AN: 3478

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: no assertion criteria provided

Pathogenic	VUS	Benign	Condition
-	1	-	Estrogen resistance syndrome (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.090
DANN	Benign	0.40
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs9397435; hg19: chr6-151951220;