rs4956302

Positions:

• chr4-141543569-A-G

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.437

Gnomad4 AMR AF: 0.327

Gnomad4 ASJ AF: 0.168

Gnomad4 EAS AF: 0.361

Gnomad4 SAS AF: 0.207

Gnomad4 FIN AF: 0.136

Gnomad4 NFE AF: 0.175

Gnomad4 OTH AF: 0.258

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4956302; hg19: chr4-142464722;