4-54541595-C-G

Variant names:

• chr4-54541595-C-G
• rs172629

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 0.169 in 152,062 control chromosomes in the GnomAD database, including 2,479 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 0.17 (2479 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.483
• Publications: 24 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 (EAS) allele frequency at 95% confidence interval = 0.32 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: 0.169 AC: 25694 AN: 151944 Hom.: 2474 Cov.: 32

Gnomad AFR AF: 0.196

Gnomad AMI AF: 0.135

Gnomad AMR AF: 0.223

Gnomad ASJ AF: 0.0963

Gnomad EAS AF: 0.333

Gnomad SAS AF: 0.271

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.127

Gnomad OTH AF: 0.167

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

GnomAD4 genome AF: 0.169 AC: 25719 AN: 152062 Hom.: 2479 Cov.: 32 AF XY: 0.174 AC XY: 12930 AN XY: 74310

African (AFR) AF: 0.196 AC: 8148 AN: 41466

American (AMR) AF: 0.223 AC: 3404 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0963 AC: 334 AN: 3470

East Asian (EAS) AF: 0.333 AC: 1722 AN: 5170

South Asian (SAS) AF: 0.271 AC: 1305 AN: 4818

European-Finnish (FIN) AF: 0.158 AC: 1674 AN: 10562

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.127 AC: 8624 AN: 67992

Other (OTH) AF: 0.167 AC: 352 AN: 2108

Alfa AF: 0.140 Hom.: 948

Bravo AF: 0.175

Asia WGS AF: 0.292 AC: 1015 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	11
DANN	Benign	0.49
PhyloP100		0.48

Splicing

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

Other links and lift over

dbSNP: rs172629; hg19: chr4-55407762;