rs2256143

Variant names:

• chr4-165625028-T-C
• rs2256143

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.832

Gnomad4 AMR AF: 0.743

Gnomad4 ASJ AF: 0.664

Gnomad4 EAS AF: 0.514

Gnomad4 SAS AF: 0.594

Gnomad4 FIN AF: 0.624

Gnomad4 NFE AF: 0.629

Gnomad4 OTH AF: 0.680

Alfa AF: 0.671 Hom.: 10704

Bravo AF: 0.706

Asia WGS AF: 0.644 AC: 2236 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2256143; hg19: chr4-166546180;