rs7848810

Variant names:

• chr9-90645576-C-A
• rs7848810

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 0.288 in 152,078 control chromosomes in the GnomAD database, including 6,483 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 0.29 (6483 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.28
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.343 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: 0.289 AC: 43848 AN: 151960 Hom.: 6487 Cov.: 32

Gnomad AFR AF: 0.271

Gnomad AMI AF: 0.271

Gnomad AMR AF: 0.244

Gnomad ASJ AF: 0.342

Gnomad EAS AF: 0.356

Gnomad SAS AF: 0.357

Gnomad FIN AF: 0.276

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.296

Gnomad OTH AF: 0.341

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

GnomAD4 genome AF: 0.288 AC: 43850 AN: 152078 Hom.: 6483 Cov.: 32 AF XY: 0.291 AC XY: 21603 AN XY: 74340

African (AFR) AF: 0.271 AC: 11226 AN: 41460

American (AMR) AF: 0.244 AC: 3734 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.342 AC: 1186 AN: 3470

East Asian (EAS) AF: 0.356 AC: 1841 AN: 5168

South Asian (SAS) AF: 0.357 AC: 1722 AN: 4822

European-Finnish (FIN) AF: 0.276 AC: 2914 AN: 10566

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.296 AC: 20137 AN: 67986

Other (OTH) AF: 0.340 AC: 719 AN: 2112

Alfa AF: 0.284 Hom.: 2669

Bravo AF: 0.285

Asia WGS AF: 0.299 AC: 1039 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.8
DANN	Benign	0.61
PhyloP100		2.3

Splicing

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

Other links and lift over

dbSNP: rs7848810; hg19: chr9-93407858; COSMIC: COSV65370186;