rs7681423

Variant names:

• chr4-154621096-C-T
• rs7681423

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 0.262 in 152,052 control chromosomes in the GnomAD database, including 5,483 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 0.26 (5483 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.232
• Publications: 19 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.433 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: 0.262 AC: 39758 AN: 151934 Hom.: 5480 Cov.: 33

Gnomad AFR AF: 0.263

Gnomad AMI AF: 0.255

Gnomad AMR AF: 0.220

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.448

Gnomad SAS AF: 0.288

Gnomad FIN AF: 0.349

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.248

Gnomad OTH AF: 0.218

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

GnomAD4 genome AF: 0.262 AC: 39781 AN: 152052 Hom.: 5483 Cov.: 33 AF XY: 0.266 AC XY: 19760 AN XY: 74322

African (AFR) AF: 0.263 AC: 10917 AN: 41476

American (AMR) AF: 0.219 AC: 3348 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.148 AC: 513 AN: 3468

East Asian (EAS) AF: 0.448 AC: 2316 AN: 5170

South Asian (SAS) AF: 0.288 AC: 1388 AN: 4818

European-Finnish (FIN) AF: 0.349 AC: 3679 AN: 10554

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.248 AC: 16884 AN: 67972

Other (OTH) AF: 0.217 AC: 458 AN: 2114

Alfa AF: 0.252 Hom.: 9714

Bravo AF: 0.253

Asia WGS AF: 0.315 AC: 1093 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.0
DANN	Benign	0.73
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs7681423; hg19: chr4-155542248;