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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901435	XR_007059816.1	n.3408+103A>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: no assertion criteria provided

Submissions by phenotype

Estrogen resistance syndrome Uncertain:1

Mar 01, 2014

Department of Breast and Endocrine Surgery, Kumamoto University

Significance: Uncertain significance

Review Status: no assertion criteria provided

Collection Method: research

- -

Computational scores

Source: dbNSFP v4.3

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;