7-127300567-A-G

Variant names:

• chr7-127300567-A-G
• rs10259338

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 0.582 in 151,982 control chromosomes in the GnomAD database, including 28,701 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 0.58 (28701 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.502
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.86 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.582 AC: 88421 AN: 151864 Hom.: 28658 Cov.: 32

Gnomad AFR AF: 0.867

Gnomad AMI AF: 0.598

Gnomad AMR AF: 0.487

Gnomad ASJ AF: 0.693

Gnomad EAS AF: 0.167

Gnomad SAS AF: 0.380

Gnomad FIN AF: 0.395

Gnomad MID AF: 0.709

Gnomad NFE AF: 0.499

Gnomad OTH AF: 0.589

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

GnomAD4 genome AF: 0.582 AC: 88504 AN: 151982 Hom.: 28701 Cov.: 32 AF XY: 0.569 AC XY: 42300 AN XY: 74316

African (AFR) AF: 0.867 AC: 35971 AN: 41468

American (AMR) AF: 0.486 AC: 7412 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.693 AC: 2404 AN: 3470

East Asian (EAS) AF: 0.167 AC: 862 AN: 5174

South Asian (SAS) AF: 0.378 AC: 1820 AN: 4820

European-Finnish (FIN) AF: 0.395 AC: 4170 AN: 10560

Middle Eastern (MID) AF: 0.701 AC: 206 AN: 294

European-Non Finnish (NFE) AF: 0.499 AC: 33884 AN: 67918

Other (OTH) AF: 0.584 AC: 1232 AN: 2110

Alfa AF: 0.552 Hom.: 4333

Bravo AF: 0.603

Asia WGS AF: 0.323 AC: 1125 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.9
DANN	Benign	0.56
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs10259338; hg19: chr7-126940621;