4-64142664-G-A

Variant names:

• chr4-64142664-G-A
• rs4860568

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 0.13 in 152,062 control chromosomes in the GnomAD database, including 1,375 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 0.13 (1375 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.137
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.16 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: 0.130 AC: 19760 AN: 151942 Hom.: 1371 Cov.: 33

Gnomad AFR AF: 0.0861

Gnomad AMI AF: 0.0822

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.131

Gnomad FIN AF: 0.139

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.144

Gnomad OTH AF: 0.144

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

GnomAD4 genome AF: 0.130 AC: 19765 AN: 152062 Hom.: 1375 Cov.: 33 AF XY: 0.131 AC XY: 9700 AN XY: 74318

African (AFR) AF: 0.0859 AC: 3564 AN: 41486

American (AMR) AF: 0.155 AC: 2361 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.178 AC: 618 AN: 3468

East Asian (EAS) AF: 0.170 AC: 876 AN: 5168

South Asian (SAS) AF: 0.130 AC: 629 AN: 4828

European-Finnish (FIN) AF: 0.139 AC: 1463 AN: 10546

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.144 AC: 9801 AN: 67984

Other (OTH) AF: 0.143 AC: 303 AN: 2116

Alfa AF: 0.127 Hom.: 195

Bravo AF: 0.131

Asia WGS AF: 0.135 AC: 468 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.5
DANN	Benign	0.86
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs4860568; hg19: chr4-65008382;