chr6-46183494-C-T

Variant names:

• chr6-46183494-C-T
• rs6925476

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 0.232 in 152,124 control chromosomes in the GnomAD database, including 4,239 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 0.23 (4239 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.60
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.245 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: 0.232 AC: 35274 AN: 152006 Hom.: 4236 Cov.: 32

Gnomad AFR AF: 0.246

Gnomad AMI AF: 0.169

Gnomad AMR AF: 0.198

Gnomad ASJ AF: 0.219

Gnomad EAS AF: 0.131

Gnomad SAS AF: 0.194

Gnomad FIN AF: 0.200

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.248

Gnomad OTH AF: 0.239

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

GnomAD4 genome AF: 0.232 AC: 35294 AN: 152124 Hom.: 4239 Cov.: 32 AF XY: 0.227 AC XY: 16885 AN XY: 74336

African (AFR) AF: 0.246 AC: 10219 AN: 41520

American (AMR) AF: 0.198 AC: 3027 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.219 AC: 759 AN: 3468

East Asian (EAS) AF: 0.131 AC: 677 AN: 5172

South Asian (SAS) AF: 0.194 AC: 936 AN: 4828

European-Finnish (FIN) AF: 0.200 AC: 2114 AN: 10554

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.248 AC: 16863 AN: 67990

Other (OTH) AF: 0.235 AC: 497 AN: 2114

Alfa AF: 0.242 Hom.: 19957

Bravo AF: 0.232

Asia WGS AF: 0.176 AC: 614 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.067
DANN	Benign	0.39
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs6925476; hg19: chr6-46151231;