rs7654093

Variant names:

• chr4-154623920-A-T
• rs7654093

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 0.269 in 151,342 control chromosomes in the GnomAD database, including 5,719 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 0.27 (5719 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.15
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.448 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: 0.269 AC: 40621 AN: 151228 Hom.: 5719 Cov.: 31

Gnomad AFR AF: 0.305

Gnomad AMI AF: 0.257

Gnomad AMR AF: 0.223

Gnomad ASJ AF: 0.142

Gnomad EAS AF: 0.464

Gnomad SAS AF: 0.293

Gnomad FIN AF: 0.308

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.243

Gnomad OTH AF: 0.228

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

GnomAD4 genome AF: 0.269 AC: 40642 AN: 151342 Hom.: 5719 Cov.: 31 AF XY: 0.271 AC XY: 20040 AN XY: 73922

African (AFR) AF: 0.305 AC: 12562 AN: 41246

American (AMR) AF: 0.223 AC: 3382 AN: 15180

Ashkenazi Jewish (ASJ) AF: 0.142 AC: 493 AN: 3464

East Asian (EAS) AF: 0.464 AC: 2378 AN: 5128

South Asian (SAS) AF: 0.294 AC: 1400 AN: 4764

European-Finnish (FIN) AF: 0.308 AC: 3229 AN: 10486

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.243 AC: 16443 AN: 67768

Other (OTH) AF: 0.226 AC: 476 AN: 2104

Alfa AF: 0.248 Hom.: 639

Bravo AF: 0.264

Asia WGS AF: 0.323 AC: 1119 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	2.8
DANN	Benign	0.82
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs7654093; hg19: chr4-155545072;