rs12665607

chr6-151625494-T-Achr6-151625494-T-C

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 0.0679 in 152,254 control chromosomes in the GnomAD database, including 578 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 0.068 (578 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Uncertain significance no assertion criteria provided U:1
• Conservation: PhyloP100: 0.714

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• 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	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0680 AC: 10348 AN: 152136 Hom.: 579 Cov.: 32

Gnomad AFR AF: 0.0255

Gnomad AMI AF: 0.0374

Gnomad AMR AF: 0.0691

Gnomad ASJ AF: 0.0951

Gnomad EAS AF: 0.302

Gnomad SAS AF: 0.0850

Gnomad FIN AF: 0.0263

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.0791

Gnomad OTH AF: 0.0932

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

GnomAD4 genome AF: 0.0679 AC: 10340 AN: 152254 Hom.: 578 Cov.: 32 AF XY: 0.0670 AC XY: 4987 AN XY: 74432

Gnomad4 AFR AF: 0.0254

Gnomad4 AMR AF: 0.0690

Gnomad4 ASJ AF: 0.0951

Gnomad4 EAS AF: 0.302

Gnomad4 SAS AF: 0.0853

Gnomad4 FIN AF: 0.0263

Gnomad4 NFE AF: 0.0790

Gnomad4 OTH AF: 0.0932

Alfa AF: 0.0616 Hom.: 46

Bravo AF: 0.0704

Asia WGS AF: 0.170 AC: 589 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	-0.82
Cadd	Benign	8.3
Dann	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12665607; hg19: chr6-151946629;