chr6-133107794-G-A

Variant names:

• chr6-133107794-G-A
• rs4273707

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 0.308 in 152,090 control chromosomes in the GnomAD database, including 10,825 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.31 (10825 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00400
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.647 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: 0.308 AC: 46818 AN: 151972 Hom.: 10802 Cov.: 32

Gnomad AFR AF: 0.654

Gnomad AMI AF: 0.139

Gnomad AMR AF: 0.202

Gnomad ASJ AF: 0.106

Gnomad EAS AF: 0.210

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.178

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.179

Gnomad OTH AF: 0.260

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

GnomAD4 genome AF: 0.308 AC: 46892 AN: 152090 Hom.: 10825 Cov.: 32 AF XY: 0.303 AC XY: 22529 AN XY: 74358

African (AFR) AF: 0.654 AC: 27090 AN: 41450

American (AMR) AF: 0.201 AC: 3074 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.106 AC: 369 AN: 3468

East Asian (EAS) AF: 0.211 AC: 1091 AN: 5178

South Asian (SAS) AF: 0.103 AC: 498 AN: 4820

European-Finnish (FIN) AF: 0.178 AC: 1889 AN: 10590

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.179 AC: 12165 AN: 68002

Other (OTH) AF: 0.257 AC: 544 AN: 2114

Alfa AF: 0.200 Hom.: 2021

Bravo AF: 0.323

Asia WGS AF: 0.197 AC: 686 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.2
DANN	Benign	0.54
PhyloP100		-0.0040

Splicing

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

Other links and lift over

dbSNP: rs4273707; hg19: chr6-133428933;