10-89058620-T-C

Variant names:

• chr10-89058620-T-C
• rs7920888

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 0.461 in 152,150 control chromosomes in the GnomAD database, including 16,441 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 0.46 (16441 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.113
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.503 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.461 AC: 70119 AN: 152032 Hom.: 16428 Cov.: 33

Gnomad AFR AF: 0.509

Gnomad AMI AF: 0.478

Gnomad AMR AF: 0.492

Gnomad ASJ AF: 0.357

Gnomad EAS AF: 0.282

Gnomad SAS AF: 0.420

Gnomad FIN AF: 0.383

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.460

Gnomad OTH AF: 0.451

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

GnomAD4 genome AF: 0.461 AC: 70173 AN: 152150 Hom.: 16441 Cov.: 33 AF XY: 0.456 AC XY: 33913 AN XY: 74370

African (AFR) AF: 0.509 AC: 21151 AN: 41548

American (AMR) AF: 0.493 AC: 7529 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.357 AC: 1237 AN: 3468

East Asian (EAS) AF: 0.282 AC: 1460 AN: 5176

South Asian (SAS) AF: 0.419 AC: 2024 AN: 4826

European-Finnish (FIN) AF: 0.383 AC: 4049 AN: 10566

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.460 AC: 31231 AN: 67960

Other (OTH) AF: 0.447 AC: 945 AN: 2114

Alfa AF: 0.458 Hom.: 51704

Bravo AF: 0.469

Asia WGS AF: 0.359 AC: 1245 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	5.4
DANN	Benign	0.70
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs7920888; hg19: chr10-90818377;