rs2256700

Positions:

• chr10-99873690-A-G

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;