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. The variant received -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
• Publications: 12 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.505 AC: 20917 AN: 41394

American (AMR) AF: 0.595 AC: 9049 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.664 AC: 2299 AN: 3464

East Asian (EAS) AF: 0.409 AC: 2098 AN: 5126

South Asian (SAS) AF: 0.502 AC: 2414 AN: 4808

European-Finnish (FIN) AF: 0.613 AC: 6458 AN: 10540

Middle Eastern (MID) AF: 0.728 AC: 214 AN: 294

European-Non Finnish (NFE) AF: 0.708 AC: 48093 AN: 67918

Other (OTH) AF: 0.610 AC: 1287 AN: 2110

Alfa AF: 0.651 Hom.: 9447

Bravo AF: 0.610

Asia WGS AF: 0.432 AC: 1504 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.36
DANN	Benign	0.46
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs1416406; hg19: chr10-109044871;