rs999473

Variant names:

• chr10-44686868-A-G
• rs999473

Your query was ambiguous. Multiple possible variants found:

• chr10-44686868-A-G
• chr10-44686868-A-T

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 0.375 in 152,064 control chromosomes in the GnomAD database, including 12,743 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 0.38 (12743 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0280

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.614 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: 0.375 AC: 57008 AN: 151946 Hom.: 12708 Cov.: 32

Gnomad AFR AF: 0.620

Gnomad AMI AF: 0.352

Gnomad AMR AF: 0.253

Gnomad ASJ AF: 0.281

Gnomad EAS AF: 0.499

Gnomad SAS AF: 0.252

Gnomad FIN AF: 0.234

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.282

Gnomad OTH AF: 0.345

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

GnomAD4 genome AF: 0.375 AC: 57089 AN: 152064 Hom.: 12743 Cov.: 32 AF XY: 0.369 AC XY: 27424 AN XY: 74342

Gnomad4 AFR AF: 0.620

Gnomad4 AMR AF: 0.253

Gnomad4 ASJ AF: 0.281

Gnomad4 EAS AF: 0.498

Gnomad4 SAS AF: 0.251

Gnomad4 FIN AF: 0.234

Gnomad4 NFE AF: 0.282

Gnomad4 OTH AF: 0.342

Alfa AF: 0.285 Hom.: 13253

Bravo AF: 0.391

Asia WGS AF: 0.385 AC: 1337 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.0
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs999473; hg19: chr10-45182316;