7-127606849-G-A

Variant names:

• chr7-127606849-G-A
• rs10229583

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 0.233 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
• Publications: 54 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 (SAS) allele frequency at 95% confidence interval = 0.311 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.234 AC: 9702 AN: 41528

American (AMR) AF: 0.186 AC: 2837 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.174 AC: 604 AN: 3470

East Asian (EAS) AF: 0.159 AC: 825 AN: 5178

South Asian (SAS) AF: 0.325 AC: 1565 AN: 4820

European-Finnish (FIN) AF: 0.265 AC: 2797 AN: 10572

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.242 AC: 16485 AN: 67998

Other (OTH) AF: 0.212 AC: 448 AN: 2110

Alfa AF: 0.231 Hom.: 14745

Bravo AF: 0.222

Asia WGS AF: 0.225 AC: 785 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.8
DANN	Benign	0.41
PhyloP100		0.41

Splicing

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

Other links and lift over

dbSNP: rs10229583; hg19: chr7-127246903;