rs2256700

Variant names:

• chr10-99873690-A-G
• rs2256700

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 0.132 in 152,120 control chromosomes in the GnomAD database, including 1,951 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 0.13 (1951 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.985

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 = 0.262 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: 0.132 AC: 19995 AN: 152002 Hom.: 1951 Cov.: 32

Gnomad AFR AF: 0.266

Gnomad AMI AF: 0.0297

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.0767

Gnomad EAS AF: 0.0214

Gnomad SAS AF: 0.116

Gnomad FIN AF: 0.0593

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0810

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.132 AC: 20027 AN: 152120 Hom.: 1951 Cov.: 32 AF XY: 0.129 AC XY: 9627 AN XY: 74402

Gnomad4 AFR AF: 0.266

Gnomad4 AMR AF: 0.105

Gnomad4 ASJ AF: 0.0767

Gnomad4 EAS AF: 0.0214

Gnomad4 SAS AF: 0.116

Gnomad4 FIN AF: 0.0593

Gnomad4 NFE AF: 0.0810

Gnomad4 OTH AF: 0.130

Alfa AF: 0.0908 Hom.: 1460

Bravo AF: 0.141

Asia WGS AF: 0.102 AC: 355 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.1
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2256700; hg19: chr10-101633447;