6-46149567-C-T

Variant names:

• chr6-46149567-C-T
• rs9472702

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 0.0779 in 152,006 control chromosomes in the GnomAD database, including 521 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 0.078 (521 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0910
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.153 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: 0.0779 AC: 11830 AN: 151888 Hom.: 520 Cov.: 32

Gnomad AFR AF: 0.0769

Gnomad AMI AF: 0.0362

Gnomad AMR AF: 0.0674

Gnomad ASJ AF: 0.0698

Gnomad EAS AF: 0.162

Gnomad SAS AF: 0.0191

Gnomad FIN AF: 0.164

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0666

Gnomad OTH AF: 0.0657

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

GnomAD4 genome AF: 0.0779 AC: 11837 AN: 152006 Hom.: 521 Cov.: 32 AF XY: 0.0810 AC XY: 6021 AN XY: 74294

African (AFR) AF: 0.0768 AC: 3184 AN: 41450

American (AMR) AF: 0.0674 AC: 1029 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0698 AC: 242 AN: 3468

East Asian (EAS) AF: 0.162 AC: 840 AN: 5172

South Asian (SAS) AF: 0.0192 AC: 92 AN: 4804

European-Finnish (FIN) AF: 0.164 AC: 1726 AN: 10552

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0666 AC: 4528 AN: 67970

Other (OTH) AF: 0.0660 AC: 139 AN: 2106

Alfa AF: 0.0645 Hom.: 178

Bravo AF: 0.0731

Asia WGS AF: 0.0770 AC: 268 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	9.3
DANN	Benign	0.81
PhyloP100		0.091

Splicing

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

Other links and lift over

dbSNP: rs9472702; hg19: chr6-46117304;