rs7898888

Positions:

• chr10-28351303-T-C

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 0.07 in 152,016 control chromosomes in the GnomAD database, including 432 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 0.070 (432 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.567

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0875 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0700 AC: 10634 AN: 151896 Hom.: 431 Cov.: 32

Gnomad AFR AF: 0.0880

Gnomad AMI AF: 0.0329

Gnomad AMR AF: 0.0480

Gnomad ASJ AF: 0.109

Gnomad EAS AF: 0.0532

Gnomad SAS AF: 0.0950

Gnomad FIN AF: 0.0189

Gnomad MID AF: 0.0828

Gnomad NFE AF: 0.0698

Gnomad OTH AF: 0.0738

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

GnomAD4 genome AF: 0.0700 AC: 10641 AN: 152016 Hom.: 432 Cov.: 32 AF XY: 0.0669 AC XY: 4970 AN XY: 74292

Gnomad4 AFR AF: 0.0880

Gnomad4 AMR AF: 0.0478

Gnomad4 ASJ AF: 0.109

Gnomad4 EAS AF: 0.0533

Gnomad4 SAS AF: 0.0947

Gnomad4 FIN AF: 0.0189

Gnomad4 NFE AF: 0.0698

Gnomad4 OTH AF: 0.0731

Alfa AF: 0.0709 Hom.: 76

Bravo AF: 0.0723

Asia WGS AF: 0.0590 AC: 206 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.4
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7898888; hg19: chr10-28640232;