4-27410203-A-T

Variant names:

• chr4-27410203-A-T
• rs210758

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.0846 in 151,824 control chromosomes in the GnomAD database, including 594 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 0.085 (594 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.46
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.21).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.137 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.0845 AC: 12826 AN: 151704 Hom.: 593 Cov.: 32

Gnomad AFR AF: 0.0962

Gnomad AMI AF: 0.236

Gnomad AMR AF: 0.0827

Gnomad ASJ AF: 0.0963

Gnomad EAS AF: 0.146

Gnomad SAS AF: 0.0731

Gnomad FIN AF: 0.0675

Gnomad MID AF: 0.0701

Gnomad NFE AF: 0.0738

Gnomad OTH AF: 0.0948

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

GnomAD4 genome AF: 0.0846 AC: 12849 AN: 151824 Hom.: 594 Cov.: 32 AF XY: 0.0845 AC XY: 6268 AN XY: 74180

African (AFR) AF: 0.0962 AC: 3987 AN: 41428

American (AMR) AF: 0.0829 AC: 1261 AN: 15204

Ashkenazi Jewish (ASJ) AF: 0.0963 AC: 334 AN: 3470

East Asian (EAS) AF: 0.146 AC: 747 AN: 5128

South Asian (SAS) AF: 0.0735 AC: 354 AN: 4814

European-Finnish (FIN) AF: 0.0675 AC: 712 AN: 10544

Middle Eastern (MID) AF: 0.0753 AC: 22 AN: 292

European-Non Finnish (NFE) AF: 0.0738 AC: 5016 AN: 67924

Other (OTH) AF: 0.0953 AC: 201 AN: 2110

Alfa AF: 0.0718 Hom.: 49

Bravo AF: 0.0893

Asia WGS AF: 0.143 AC: 495 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.21
CADD	Benign	16
DANN	Benign	0.74
PhyloP100		3.5

Splicing

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

Other links and lift over

dbSNP: rs210758; hg19: chr4-27411825;