chr4-186088950-C-T

Variant names:

• chr4-186088950-C-T
• rs4608848

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 0.662 in 151,962 control chromosomes in the GnomAD database, including 33,603 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 0.66 (33603 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02
• Publications: 18 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.729 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: 0.662 AC: 100452 AN: 151844 Hom.: 33571 Cov.: 31

Gnomad AFR AF: 0.736

Gnomad AMI AF: 0.675

Gnomad AMR AF: 0.717

Gnomad ASJ AF: 0.520

Gnomad EAS AF: 0.690

Gnomad SAS AF: 0.569

Gnomad FIN AF: 0.619

Gnomad MID AF: 0.662

Gnomad NFE AF: 0.622

Gnomad OTH AF: 0.671

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

GnomAD4 genome AF: 0.662 AC: 100540 AN: 151962 Hom.: 33603 Cov.: 31 AF XY: 0.661 AC XY: 49107 AN XY: 74258

African (AFR) AF: 0.735 AC: 30470 AN: 41428

American (AMR) AF: 0.717 AC: 10960 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.520 AC: 1801 AN: 3464

East Asian (EAS) AF: 0.691 AC: 3562 AN: 5158

South Asian (SAS) AF: 0.568 AC: 2729 AN: 4808

European-Finnish (FIN) AF: 0.619 AC: 6529 AN: 10556

Middle Eastern (MID) AF: 0.647 AC: 189 AN: 292

European-Non Finnish (NFE) AF: 0.622 AC: 42266 AN: 67960

Other (OTH) AF: 0.673 AC: 1421 AN: 2110

Alfa AF: 0.634 Hom.: 50644

Bravo AF: 0.673

Asia WGS AF: 0.652 AC: 2271 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.30
DANN	Benign	0.65
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs4608848; hg19: chr4-187010104;