rs10805209

Variant names:

• chr4-8548118-C-T
• rs10805209

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 0.309 in 152,140 control chromosomes in the GnomAD database, including 8,261 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 0.31 (8261 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.732

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 = 0.428 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: 0.309 AC: 47041 AN: 152022 Hom.: 8256 Cov.: 33

Gnomad AFR AF: 0.150

Gnomad AMI AF: 0.334

Gnomad AMR AF: 0.332

Gnomad ASJ AF: 0.353

Gnomad EAS AF: 0.444

Gnomad SAS AF: 0.428

Gnomad FIN AF: 0.430

Gnomad MID AF: 0.309

Gnomad NFE AF: 0.362

Gnomad OTH AF: 0.302

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

GnomAD4 genome AF: 0.309 AC: 47081 AN: 152140 Hom.: 8261 Cov.: 33 AF XY: 0.315 AC XY: 23427 AN XY: 74380

Gnomad4 AFR AF: 0.150

Gnomad4 AMR AF: 0.332

Gnomad4 ASJ AF: 0.353

Gnomad4 EAS AF: 0.443

Gnomad4 SAS AF: 0.429

Gnomad4 FIN AF: 0.430

Gnomad4 NFE AF: 0.362

Gnomad4 OTH AF: 0.306

Alfa AF: 0.357 Hom.: 20143

Bravo AF: 0.293

Asia WGS AF: 0.447 AC: 1551 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	1.5
DANN	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10805209; hg19: chr4-8549845;