rs1416406

Variant names:

• chr10-107285113-A-G
• rs1416406

Your query was ambiguous. Multiple possible variants found:

• chr10-107285113-A-G
• chr10-107285113-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 0.616 in 151,782 control chromosomes in the GnomAD database, including 29,553 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 0.62 (29553 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.715

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.703 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: 0.616 AC: 93476 AN: 151664 Hom.: 29537 Cov.: 31

Gnomad AFR AF: 0.505

Gnomad AMI AF: 0.768

Gnomad AMR AF: 0.595

Gnomad ASJ AF: 0.664

Gnomad EAS AF: 0.408

Gnomad SAS AF: 0.502

Gnomad FIN AF: 0.613

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.708

Gnomad OTH AF: 0.616

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

GnomAD4 genome AF: 0.616 AC: 93526 AN: 151782 Hom.: 29553 Cov.: 31 AF XY: 0.610 AC XY: 45219 AN XY: 74136

Gnomad4 AFR AF: 0.505

Gnomad4 AMR AF: 0.595

Gnomad4 ASJ AF: 0.664

Gnomad4 EAS AF: 0.409

Gnomad4 SAS AF: 0.502

Gnomad4 FIN AF: 0.613

Gnomad4 NFE AF: 0.708

Gnomad4 OTH AF: 0.610

Alfa AF: 0.641 Hom.: 4577

Bravo AF: 0.610

Asia WGS AF: 0.432 AC: 1504 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.36
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1416406; hg19: chr10-109044871;