rs607363

chr10-44266175-A-Gchr10-44266175-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 0.251 in 152,070 control chromosomes in the GnomAD database, including 6,364 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 0.25 (6364 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0890

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.454 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: 0.251 AC: 38081 AN: 151952 Hom.: 6338 Cov.: 32

Gnomad AFR AF: 0.459

Gnomad AMI AF: 0.0945

Gnomad AMR AF: 0.226

Gnomad ASJ AF: 0.195

Gnomad EAS AF: 0.345

Gnomad SAS AF: 0.354

Gnomad FIN AF: 0.156

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.244

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

GnomAD4 genome AF: 0.251 AC: 38162 AN: 152070 Hom.: 6364 Cov.: 32 AF XY: 0.254 AC XY: 18870 AN XY: 74356

Gnomad4 AFR AF: 0.460

Gnomad4 AMR AF: 0.226

Gnomad4 ASJ AF: 0.195

Gnomad4 EAS AF: 0.346

Gnomad4 SAS AF: 0.355

Gnomad4 FIN AF: 0.156

Gnomad4 NFE AF: 0.135

Gnomad4 OTH AF: 0.240

Alfa AF: 0.163 Hom.: 4085

Bravo AF: 0.265

Asia WGS AF: 0.332 AC: 1154 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	2.7
Dann	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs607363; hg19: chr10-44761623;