rs10259338

Variant names:

• chr7-127300567-A-G
• rs10259338

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 0.582 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.582 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

Gnomad4 AFR AF: 0.867

Gnomad4 AMR AF: 0.486

Gnomad4 ASJ AF: 0.693

Gnomad4 EAS AF: 0.167

Gnomad4 SAS AF: 0.378

Gnomad4 FIN AF: 0.395

Gnomad4 NFE AF: 0.499

Gnomad4 OTH AF: 0.584

Alfa AF: 0.543 Hom.: 4056

Bravo AF: 0.603

Asia WGS AF: 0.323 AC: 1125 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10259338; hg19: chr7-126940621;