rs4864976

Variant names:

• chr4-55287565-T-C
• rs4864976

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 0.221 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
• Publications: 4 publications found

ACMG classification

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

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

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.422 AC: 17492 AN: 41420

American (AMR) AF: 0.186 AC: 2845 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.131 AC: 453 AN: 3470

East Asian (EAS) AF: 0.271 AC: 1393 AN: 5136

South Asian (SAS) AF: 0.134 AC: 646 AN: 4820

European-Finnish (FIN) AF: 0.134 AC: 1419 AN: 10586

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.128 AC: 8668 AN: 67984

Other (OTH) AF: 0.216 AC: 456 AN: 2110

Alfa AF: 0.157 Hom.: 10003

Bravo AF: 0.238

Asia WGS AF: 0.212 AC: 741 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.1
DANN	Benign	0.32
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs4864976; hg19: chr4-56153732;