10-87856722-A-C

Variant names:

• chr10-87856722-A-C
• rs1234221

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 0.183 in 152,158 control chromosomes in the GnomAD database, including 3,238 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 0.18 (3238 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0990
• Publications: 17 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.365 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: 0.183 AC: 27897 AN: 152040 Hom.: 3240 Cov.: 31

Gnomad AFR AF: 0.0534

Gnomad AMI AF: 0.333

Gnomad AMR AF: 0.167

Gnomad ASJ AF: 0.257

Gnomad EAS AF: 0.262

Gnomad SAS AF: 0.379

Gnomad FIN AF: 0.215

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.235

Gnomad OTH AF: 0.194

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

GnomAD4 genome AF: 0.183 AC: 27898 AN: 152158 Hom.: 3238 Cov.: 31 AF XY: 0.187 AC XY: 13879 AN XY: 74382

African (AFR) AF: 0.0533 AC: 2214 AN: 41548

American (AMR) AF: 0.167 AC: 2544 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.257 AC: 891 AN: 3466

East Asian (EAS) AF: 0.263 AC: 1361 AN: 5178

South Asian (SAS) AF: 0.380 AC: 1831 AN: 4824

European-Finnish (FIN) AF: 0.215 AC: 2277 AN: 10572

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.235 AC: 16003 AN: 67978

Other (OTH) AF: 0.192 AC: 405 AN: 2112

Alfa AF: 0.217 Hom.: 5252

Bravo AF: 0.172

Asia WGS AF: 0.274 AC: 952 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.6
DANN	Benign	0.66
PhyloP100		0.099

Splicing

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

Other links and lift over

dbSNP: rs1234221; hg19: chr10-89616479;