rs1417374

Positions:

• chr10-22839546-G-A

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 0.24 in 152,072 control chromosomes in the GnomAD database, including 4,836 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 0.24 (4836 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.683

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.32 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: 0.240 AC: 36488 AN: 151954 Hom.: 4832 Cov.: 32

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.358

Gnomad AMR AF: 0.256

Gnomad ASJ AF: 0.260

Gnomad EAS AF: 0.168

Gnomad SAS AF: 0.334

Gnomad FIN AF: 0.265

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.294

Gnomad OTH AF: 0.232

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

GnomAD4 genome AF: 0.240 AC: 36490 AN: 152072 Hom.: 4836 Cov.: 32 AF XY: 0.240 AC XY: 17802 AN XY: 74328

Gnomad4 AFR AF: 0.133

Gnomad4 AMR AF: 0.256

Gnomad4 ASJ AF: 0.260

Gnomad4 EAS AF: 0.168

Gnomad4 SAS AF: 0.333

Gnomad4 FIN AF: 0.265

Gnomad4 NFE AF: 0.294

Gnomad4 OTH AF: 0.233

Alfa AF: 0.285 Hom.: 8367

Bravo AF: 0.231

Asia WGS AF: 0.230 AC: 797 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.3
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1417374; hg19: chr10-23128475;