chr10-101210404-T-C

Position:

• chr10-101210404-T-C

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 0.228 in 152,064 control chromosomes in the GnomAD database, including 4,370 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 0.23 (4370 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.659

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.29 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: 0.228 AC: 34692 AN: 151946 Hom.: 4364 Cov.: 32

Gnomad AFR AF: 0.175

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.192

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.0569

Gnomad SAS AF: 0.0814

Gnomad FIN AF: 0.236

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.294

Gnomad OTH AF: 0.218

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

GnomAD4 genome AF: 0.228 AC: 34704 AN: 152064 Hom.: 4370 Cov.: 32 AF XY: 0.221 AC XY: 16464 AN XY: 74336

Gnomad4 AFR AF: 0.175

Gnomad4 AMR AF: 0.192

Gnomad4 ASJ AF: 0.202

Gnomad4 EAS AF: 0.0572

Gnomad4 SAS AF: 0.0819

Gnomad4 FIN AF: 0.236

Gnomad4 NFE AF: 0.294

Gnomad4 OTH AF: 0.218

Alfa AF: 0.259 Hom.: 1870

Bravo AF: 0.226

Asia WGS AF: 0.0850 AC: 294 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.46
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7893223; hg19: chr10-102970161;