rs9803850

Variant names:

• chr1-85604761-A-C
• rs9803850

Your query was ambiguous. Multiple possible variants found:

• chr1-85604761-A-C
• chr1-85604761-A-T

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 0.257 in 152,024 control chromosomes in the GnomAD database, including 5,202 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 0.26 (5202 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0810
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.304 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: 0.257 AC: 39080 AN: 151906 Hom.: 5199 Cov.: 32

Gnomad AFR AF: 0.255

Gnomad AMI AF: 0.263

Gnomad AMR AF: 0.291

Gnomad ASJ AF: 0.259

Gnomad EAS AF: 0.316

Gnomad SAS AF: 0.173

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.257

Gnomad OTH AF: 0.273

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

GnomAD4 genome AF: 0.257 AC: 39102 AN: 152024 Hom.: 5202 Cov.: 32 AF XY: 0.255 AC XY: 18975 AN XY: 74300

African (AFR) AF: 0.255 AC: 10564 AN: 41462

American (AMR) AF: 0.291 AC: 4445 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.259 AC: 897 AN: 3466

East Asian (EAS) AF: 0.317 AC: 1631 AN: 5150

South Asian (SAS) AF: 0.173 AC: 831 AN: 4810

European-Finnish (FIN) AF: 0.225 AC: 2375 AN: 10576

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.257 AC: 17462 AN: 67978

Other (OTH) AF: 0.272 AC: 571 AN: 2102

Alfa AF: 0.255 Hom.: 1929

Bravo AF: 0.260

Asia WGS AF: 0.269 AC: 936 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	9.4
DANN	Benign	0.77
PhyloP100		-0.081

Splicing

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

Other links and lift over

dbSNP: rs9803850; hg19: chr1-86070444;