rs7898455

chr10-8696945-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 0.27 in 151,892 control chromosomes in the GnomAD database, including 6,151 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 0.27 (6151 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.371

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.342 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: 0.270 AC: 41002 AN: 151774 Hom.: 6132 Cov.: 31

Gnomad AFR AF: 0.128

Gnomad AMI AF: 0.370

Gnomad AMR AF: 0.318

Gnomad ASJ AF: 0.299

Gnomad EAS AF: 0.355

Gnomad SAS AF: 0.280

Gnomad FIN AF: 0.332

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.326

Gnomad OTH AF: 0.288

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

GnomAD4 genome AF: 0.270 AC: 41038 AN: 151892 Hom.: 6151 Cov.: 31 AF XY: 0.272 AC XY: 20214 AN XY: 74214

Gnomad4 AFR AF: 0.128

Gnomad4 AMR AF: 0.319

Gnomad4 ASJ AF: 0.299

Gnomad4 EAS AF: 0.356

Gnomad4 SAS AF: 0.280

Gnomad4 FIN AF: 0.332

Gnomad4 NFE AF: 0.326

Gnomad4 OTH AF: 0.292

Alfa AF: 0.312 Hom.: 15584

Bravo AF: 0.263

Asia WGS AF: 0.307 AC: 1066 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.52
Dann	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7898455; hg19: chr10-8738908;