chr10-101210404-T-C

Variant names:

• chr10-101210404-T-C
• rs7893223

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 0.228 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
• Publications: 4 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 (NFE) allele frequency at 95% confidence interval = 0.29 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: 0.228 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

African (AFR) AF: 0.175 AC: 7246 AN: 41484

American (AMR) AF: 0.192 AC: 2933 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.202 AC: 699 AN: 3468

East Asian (EAS) AF: 0.0572 AC: 296 AN: 5174

South Asian (SAS) AF: 0.0819 AC: 395 AN: 4822

European-Finnish (FIN) AF: 0.236 AC: 2491 AN: 10570

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.294 AC: 19969 AN: 67966

Other (OTH) AF: 0.218 AC: 459 AN: 2106

Alfa AF: 0.260 Hom.: 2298

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
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs7893223; hg19: chr10-102970161;