rs2256143

Variant names:

• chr4-165625028-T-C
• rs2256143

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 0.692 in 152,084 control chromosomes in the GnomAD database, including 37,309 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 0.69 (37309 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.821
• Publications: 3 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 = 0.825 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: 0.692 AC: 105183 AN: 151966 Hom.: 37247 Cov.: 32

Gnomad AFR AF: 0.832

Gnomad AMI AF: 0.719

Gnomad AMR AF: 0.743

Gnomad ASJ AF: 0.664

Gnomad EAS AF: 0.514

Gnomad SAS AF: 0.594

Gnomad FIN AF: 0.624

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.629

Gnomad OTH AF: 0.677

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

GnomAD4 genome AF: 0.692 AC: 105300 AN: 152084 Hom.: 37309 Cov.: 32 AF XY: 0.691 AC XY: 51354 AN XY: 74338

African (AFR) AF: 0.832 AC: 34568 AN: 41532

American (AMR) AF: 0.743 AC: 11354 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.664 AC: 2305 AN: 3470

East Asian (EAS) AF: 0.514 AC: 2656 AN: 5170

South Asian (SAS) AF: 0.594 AC: 2861 AN: 4816

European-Finnish (FIN) AF: 0.624 AC: 6601 AN: 10580

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.629 AC: 42708 AN: 67924

Other (OTH) AF: 0.680 AC: 1434 AN: 2110

Alfa AF: 0.668 Hom.: 16367

Bravo AF: 0.706

Asia WGS AF: 0.644 AC: 2236 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.2
DANN	Benign	0.48
PhyloP100		-0.82

Splicing

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

Other links and lift over

dbSNP: rs2256143; hg19: chr4-166546180;