rs56279505

Positions:

• chr4-99374083-T-A

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 0.0952 in 152,208 control chromosomes in the GnomAD database, including 777 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 0.095 (777 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.118

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.133 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: 0.0952 AC: 14480 AN: 152090 Hom.: 772 Cov.: 32

Gnomad AFR AF: 0.0558

Gnomad AMI AF: 0.0351

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.0349

Gnomad EAS AF: 0.141

Gnomad SAS AF: 0.0962

Gnomad FIN AF: 0.157

Gnomad MID AF: 0.0478

Gnomad NFE AF: 0.109

Gnomad OTH AF: 0.0840

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

GnomAD4 genome AF: 0.0952 AC: 14496 AN: 152208 Hom.: 777 Cov.: 32 AF XY: 0.0978 AC XY: 7279 AN XY: 74420

Gnomad4 AFR AF: 0.0559

Gnomad4 AMR AF: 0.102

Gnomad4 ASJ AF: 0.0349

Gnomad4 EAS AF: 0.141

Gnomad4 SAS AF: 0.0961

Gnomad4 FIN AF: 0.157

Gnomad4 NFE AF: 0.109

Gnomad4 OTH AF: 0.0865

Alfa AF: 0.104 Hom.: 113

Bravo AF: 0.0901

Asia WGS AF: 0.120 AC: 416 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	13
DANN	Benign	0.94

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs56279505; hg19: chr4-100295240;