rs7898888

Variant names:

• chr10-28351303-T-C
• rs7898888

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 0.07 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.0880 AC: 3649 AN: 41446

American (AMR) AF: 0.0478 AC: 729 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.109 AC: 379 AN: 3466

East Asian (EAS) AF: 0.0533 AC: 274 AN: 5138

South Asian (SAS) AF: 0.0947 AC: 455 AN: 4806

European-Finnish (FIN) AF: 0.0189 AC: 200 AN: 10580

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0698 AC: 4748 AN: 68002

Other (OTH) AF: 0.0731 AC: 154 AN: 2108

Alfa AF: 0.0707 Hom.: 78

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
PhyloP100		-0.57

Splicing

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

Other links and lift over

dbSNP: rs7898888; hg19: chr10-28640232;