chr10-84226798-G-C

Variant names:

• chr10-84226798-G-C
• rs745480

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 0.588 in 151,962 control chromosomes in the GnomAD database, including 27,428 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 0.59 (27428 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.664
• Publications: 15 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.77 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: 0.588 AC: 89287 AN: 151844 Hom.: 27371 Cov.: 32

Gnomad AFR AF: 0.777

Gnomad AMI AF: 0.340

Gnomad AMR AF: 0.582

Gnomad ASJ AF: 0.571

Gnomad EAS AF: 0.402

Gnomad SAS AF: 0.477

Gnomad FIN AF: 0.469

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.520

Gnomad OTH AF: 0.568

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

GnomAD4 genome AF: 0.588 AC: 89407 AN: 151962 Hom.: 27428 Cov.: 32 AF XY: 0.583 AC XY: 43310 AN XY: 74272

African (AFR) AF: 0.777 AC: 32206 AN: 41448

American (AMR) AF: 0.582 AC: 8888 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.571 AC: 1984 AN: 3472

East Asian (EAS) AF: 0.402 AC: 2075 AN: 5158

South Asian (SAS) AF: 0.477 AC: 2298 AN: 4822

European-Finnish (FIN) AF: 0.469 AC: 4948 AN: 10540

Middle Eastern (MID) AF: 0.497 AC: 146 AN: 294

European-Non Finnish (NFE) AF: 0.520 AC: 35355 AN: 67946

Other (OTH) AF: 0.571 AC: 1197 AN: 2096

Alfa AF: 0.558 Hom.: 3029

Bravo AF: 0.607

Asia WGS AF: 0.497 AC: 1728 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	1.1
DANN	Benign	0.71
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs745480; hg19: chr10-85986554;