rs1416572

chr9-12187104-A-Gchr9-12187104-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 0.692 in 151,834 control chromosomes in the GnomAD database, including 36,901 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 0.69 (36901 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0480

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.737 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: 0.692 AC: 104949 AN: 151716 Hom.: 36882 Cov.: 32

Gnomad AFR AF: 0.674

Gnomad AMI AF: 0.815

Gnomad AMR AF: 0.606

Gnomad ASJ AF: 0.797

Gnomad EAS AF: 0.381

Gnomad SAS AF: 0.622

Gnomad FIN AF: 0.690

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.743

Gnomad OTH AF: 0.693

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

GnomAD4 genome AF: 0.692 AC: 105013 AN: 151834 Hom.: 36901 Cov.: 32 AF XY: 0.685 AC XY: 50793 AN XY: 74188

Gnomad4 AFR AF: 0.674

Gnomad4 AMR AF: 0.606

Gnomad4 ASJ AF: 0.797

Gnomad4 EAS AF: 0.381

Gnomad4 SAS AF: 0.623

Gnomad4 FIN AF: 0.690

Gnomad4 NFE AF: 0.743

Gnomad4 OTH AF: 0.687

Alfa AF: 0.715 Hom.: 25134

Bravo AF: 0.683

Asia WGS AF: 0.470 AC: 1639 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	2.0
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: rs1416572; hg19: chr9-12187104;