rs4956302

Variant names:

• chr4-141543569-A-G
• rs4956302

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 0.267 in 152,066 control chromosomes in the GnomAD database, including 6,548 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 (6548 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.431 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: 0.267 AC: 40512 AN: 151948 Hom.: 6517 Cov.: 32

Gnomad AFR AF: 0.436

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.327

Gnomad ASJ AF: 0.168

Gnomad EAS AF: 0.360

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.136

Gnomad MID AF: 0.232

Gnomad NFE AF: 0.175

Gnomad OTH AF: 0.258

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

GnomAD4 genome AF: 0.267 AC: 40603 AN: 152066 Hom.: 6548 Cov.: 32 AF XY: 0.266 AC XY: 19780 AN XY: 74360

African (AFR) AF: 0.437 AC: 18096 AN: 41444

American (AMR) AF: 0.327 AC: 4999 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.168 AC: 582 AN: 3464

East Asian (EAS) AF: 0.361 AC: 1866 AN: 5176

South Asian (SAS) AF: 0.207 AC: 1000 AN: 4824

European-Finnish (FIN) AF: 0.136 AC: 1440 AN: 10588

Middle Eastern (MID) AF: 0.250 AC: 73 AN: 292

European-Non Finnish (NFE) AF: 0.175 AC: 11905 AN: 67978

Other (OTH) AF: 0.258 AC: 545 AN: 2112

Alfa AF: 0.245 Hom.: 906

Bravo AF: 0.290

Asia WGS AF: 0.267 AC: 931 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.48
DANN	Benign	0.57
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs4956302; hg19: chr4-142464722;