chr4-33224244-C-T

Variant names:

• chr4-33224244-C-T
• rs2687427

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 0.581 in 152,076 control chromosomes in the GnomAD database, including 31,594 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 0.58 (31594 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.185
• Publications: 2 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 (NFE) allele frequency at 95% confidence interval = 0.787 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: 0.582 AC: 88447 AN: 151956 Hom.: 31612 Cov.: 32

Gnomad AFR AF: 0.148

Gnomad AMI AF: 0.750

Gnomad AMR AF: 0.581

Gnomad ASJ AF: 0.787

Gnomad EAS AF: 0.625

Gnomad SAS AF: 0.641

Gnomad FIN AF: 0.783

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.793

Gnomad OTH AF: 0.624

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

GnomAD4 genome AF: 0.581 AC: 88428 AN: 152076 Hom.: 31594 Cov.: 32 AF XY: 0.582 AC XY: 43280 AN XY: 74334

African (AFR) AF: 0.147 AC: 6114 AN: 41460

American (AMR) AF: 0.581 AC: 8871 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.787 AC: 2731 AN: 3472

East Asian (EAS) AF: 0.625 AC: 3222 AN: 5158

South Asian (SAS) AF: 0.641 AC: 3095 AN: 4828

European-Finnish (FIN) AF: 0.783 AC: 8271 AN: 10562

Middle Eastern (MID) AF: 0.697 AC: 205 AN: 294

European-Non Finnish (NFE) AF: 0.793 AC: 53932 AN: 68002

Other (OTH) AF: 0.618 AC: 1303 AN: 2110

Alfa AF: 0.717 Hom.: 51512

Bravo AF: 0.546

Asia WGS AF: 0.585 AC: 2032 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	7.8
DANN	Benign	0.68
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs2687427; hg19: chr4-33225866;