6-151625494-T-A

Variant names:

• chr6-151625494-T-A
• rs12665607

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 25 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0254 AC: 1056 AN: 41564

American (AMR) AF: 0.0690 AC: 1055 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0951 AC: 330 AN: 3470

East Asian (EAS) AF: 0.302 AC: 1559 AN: 5170

South Asian (SAS) AF: 0.0853 AC: 411 AN: 4820

European-Finnish (FIN) AF: 0.0263 AC: 279 AN: 10608

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.0790 AC: 5376 AN: 68008

Other (OTH) AF: 0.0932 AC: 197 AN: 2114

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

Mar 01, 2014

Department of Breast and Endocrine Surgery, Kumamoto University

Significance: Uncertain significance

Review Status: no assertion criteria provided

Collection Method: research

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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
PhyloP100		0.71

Splicing

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

Other links and lift over

dbSNP: rs12665607; hg19: chr6-151946629;