rs1856801

Variant names:

• chr10-110632404-G-T
• rs1856801

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 0.136 in 152,182 control chromosomes in the GnomAD database, including 1,477 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 0.14 (1477 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.642
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.174 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.136 AC: 20662 AN: 152064 Hom.: 1476 Cov.: 32

Gnomad AFR AF: 0.177

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.0926

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.104

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.129

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

GnomAD4 genome AF: 0.136 AC: 20699 AN: 152182 Hom.: 1477 Cov.: 32 AF XY: 0.136 AC XY: 10124 AN XY: 74408

African (AFR) AF: 0.178 AC: 7363 AN: 41480

American (AMR) AF: 0.105 AC: 1599 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0926 AC: 321 AN: 3468

East Asian (EAS) AF: 0.169 AC: 875 AN: 5184

South Asian (SAS) AF: 0.154 AC: 742 AN: 4826

European-Finnish (FIN) AF: 0.104 AC: 1105 AN: 10606

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.122 AC: 8283 AN: 68006

Other (OTH) AF: 0.132 AC: 278 AN: 2112

Alfa AF: 0.126 Hom.: 4661

Bravo AF: 0.138

Asia WGS AF: 0.183 AC: 637 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	8.3
DANN	Benign	0.78
PhyloP100		0.64

Splicing

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

Other links and lift over

dbSNP: rs1856801; hg19: chr10-112392162;