rs4864976

Positions:

• chr4-55287565-T-C

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 0.221 in 152,016 control chromosomes in the GnomAD database, including 4,992 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 0.22 (4992 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.256

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.417 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.221 AC: 33545 AN: 151898 Hom.: 4976 Cov.: 32

Gnomad AFR AF: 0.422

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.186

Gnomad ASJ AF: 0.131

Gnomad EAS AF: 0.271

Gnomad SAS AF: 0.134

Gnomad FIN AF: 0.134

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.218

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

GnomAD4 genome AF: 0.221 AC: 33597 AN: 152016 Hom.: 4992 Cov.: 32 AF XY: 0.219 AC XY: 16258 AN XY: 74300

Gnomad4 AFR AF: 0.422

Gnomad4 AMR AF: 0.186

Gnomad4 ASJ AF: 0.131

Gnomad4 EAS AF: 0.271

Gnomad4 SAS AF: 0.134

Gnomad4 FIN AF: 0.134

Gnomad4 NFE AF: 0.128

Gnomad4 OTH AF: 0.216

Alfa AF: 0.144 Hom.: 3718

Bravo AF: 0.238

Asia WGS AF: 0.212 AC: 741 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.1
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4864976; hg19: chr4-56153732;