rs9397435

Positions:

• chr6-151630085-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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: intergenic_region
• Clinical Significance: Uncertain significance no assertion criteria provided U:1
• Conservation: PhyloP100: -1.70

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
		n.151630085A>G		intergenic_region
LOC124901435	XR_007059816.1	n.3408+103A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.0832

Gnomad4 AMR AF: 0.0636

Gnomad4 ASJ AF: 0.0832

Gnomad4 EAS AF: 0.302

Gnomad4 SAS AF: 0.0837

Gnomad4 FIN AF: 0.0261

Gnomad4 NFE AF: 0.0700

Gnomad4 OTH AF: 0.0926

Alfa AF: 0.0672 Hom.: 124

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

Uncertain significance, no assertion criteria provided

research

Department of Breast and Endocrine Surgery, Kumamoto University

Mar 01, 2014

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Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9397435; hg19: chr6-151951220;