chr6-154626274-A-G

Variant names:

• chr6-154626274-A-G
• rs955333

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 0.131 in 152,220 control chromosomes in the GnomAD database, including 1,697 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 0.13 (1697 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.330
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.179 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: 0.131 AC: 19894 AN: 152102 Hom.: 1701 Cov.: 32

Gnomad AFR AF: 0.0272

Gnomad AMI AF: 0.114

Gnomad AMR AF: 0.157

Gnomad ASJ AF: 0.242

Gnomad EAS AF: 0.189

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.247

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.152

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

GnomAD4 genome AF: 0.131 AC: 19875 AN: 152220 Hom.: 1697 Cov.: 32 AF XY: 0.137 AC XY: 10167 AN XY: 74416

African (AFR) AF: 0.0271 AC: 1127 AN: 41570

American (AMR) AF: 0.156 AC: 2390 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.242 AC: 839 AN: 3470

East Asian (EAS) AF: 0.189 AC: 978 AN: 5184

South Asian (SAS) AF: 0.129 AC: 620 AN: 4820

European-Finnish (FIN) AF: 0.247 AC: 2609 AN: 10584

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.159 AC: 10842 AN: 67988

Other (OTH) AF: 0.149 AC: 315 AN: 2112

Alfa AF: 0.143 Hom.: 330

Bravo AF: 0.122

Asia WGS AF: 0.147 AC: 510 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.33
DANN	Benign	0.57
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs955333; hg19: chr6-154947408;