rs999473

chr10-44686868-A-Gchr10-44686868-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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;