rs10027628

Variant names:

• chr4-94722806-T-C
• rs10027628

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 0.0712 in 152,220 control chromosomes in the GnomAD database, including 1,017 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 0.071 (1017 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.355
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.21 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: 0.0710 AC: 10798 AN: 152104 Hom.: 1007 Cov.: 32

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.0439

Gnomad AMR AF: 0.0289

Gnomad ASJ AF: 0.0413

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0135

Gnomad FIN AF: 0.0232

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0133

Gnomad OTH AF: 0.0560

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

GnomAD4 genome AF: 0.0712 AC: 10844 AN: 152220 Hom.: 1017 Cov.: 32 AF XY: 0.0695 AC XY: 5177 AN XY: 74440

African (AFR) AF: 0.214 AC: 8877 AN: 41474

American (AMR) AF: 0.0289 AC: 442 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0413 AC: 143 AN: 3466

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5188

South Asian (SAS) AF: 0.0137 AC: 66 AN: 4828

European-Finnish (FIN) AF: 0.0232 AC: 246 AN: 10616

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0133 AC: 903 AN: 68028

Other (OTH) AF: 0.0555 AC: 117 AN: 2110

Alfa AF: 0.0572 Hom.: 617

Bravo AF: 0.0779

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.1
DANN	Benign	0.69
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs10027628; hg19: chr4-95643957;