4-27910121-T-A

Variant names:

• chr4-27910121-T-A
• rs1035093

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 0.0362 in 152,060 control chromosomes in the GnomAD database, including 218 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 0.036 (218 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0610
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0875 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.0361 AC: 5485 AN: 151942 Hom.: 216 Cov.: 32

Gnomad AFR AF: 0.0895

Gnomad AMI AF: 0.0318

Gnomad AMR AF: 0.0245

Gnomad ASJ AF: 0.00144

Gnomad EAS AF: 0.0122

Gnomad SAS AF: 0.0416

Gnomad FIN AF: 0.0329

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0103

Gnomad OTH AF: 0.0268

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

GnomAD4 genome AF: 0.0362 AC: 5506 AN: 152060 Hom.: 218 Cov.: 32 AF XY: 0.0373 AC XY: 2771 AN XY: 74342

African (AFR) AF: 0.0899 AC: 3730 AN: 41498

American (AMR) AF: 0.0245 AC: 374 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.00144 AC: 5 AN: 3464

East Asian (EAS) AF: 0.0121 AC: 62 AN: 5142

South Asian (SAS) AF: 0.0411 AC: 198 AN: 4822

European-Finnish (FIN) AF: 0.0329 AC: 349 AN: 10610

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0103 AC: 697 AN: 67938

Other (OTH) AF: 0.0265 AC: 56 AN: 2112

Alfa AF: 0.0262 Hom.: 13

Bravo AF: 0.0373

Asia WGS AF: 0.0390 AC: 135 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.76
DANN	Benign	0.51
PhyloP100		0.061

Splicing

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

Other links and lift over

dbSNP: rs1035093; hg19: chr4-27911743;