rs10229583

chr7-127606849-G-Achr7-127606849-G-T

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 0.233 in 152,158 control chromosomes in the GnomAD database, including 4,204 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 (4204 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.414

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 (SAS) allele frequency at 95% confidence interval = 0.311 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: 0.233 AC: 35414 AN: 152040 Hom.: 4200 Cov.: 32

Gnomad AFR AF: 0.233

Gnomad AMI AF: 0.138

Gnomad AMR AF: 0.186

Gnomad ASJ AF: 0.174

Gnomad EAS AF: 0.160

Gnomad SAS AF: 0.326

Gnomad FIN AF: 0.265

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.215

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

GnomAD4 genome AF: 0.233 AC: 35438 AN: 152158 Hom.: 4204 Cov.: 32 AF XY: 0.234 AC XY: 17432 AN XY: 74374

Gnomad4 AFR AF: 0.234

Gnomad4 AMR AF: 0.186

Gnomad4 ASJ AF: 0.174

Gnomad4 EAS AF: 0.159

Gnomad4 SAS AF: 0.325

Gnomad4 FIN AF: 0.265

Gnomad4 NFE AF: 0.242

Gnomad4 OTH AF: 0.212

Alfa AF: 0.226 Hom.: 6011

Bravo AF: 0.222

Asia WGS AF: 0.225 AC: 785 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	5.8
Dann	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10229583; hg19: chr7-127246903;