rs2906066

Positions:

• chr5-142200712-A-G
• chr5-142200712-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 0.923 in 152,116 control chromosomes in the GnomAD database, including 64,955 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 0.92 (64955 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.392

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.973 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.923 AC: 140295 AN: 151996 Hom.: 64888 Cov.: 30

Gnomad AFR AF: 0.981

Gnomad AMI AF: 0.967

Gnomad AMR AF: 0.930

Gnomad ASJ AF: 0.822

Gnomad EAS AF: 0.930

Gnomad SAS AF: 0.891

Gnomad FIN AF: 0.920

Gnomad MID AF: 0.813

Gnomad NFE AF: 0.894

Gnomad OTH AF: 0.902

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

GnomAD4 genome AF: 0.923 AC: 140422 AN: 152116 Hom.: 64955 Cov.: 30 AF XY: 0.923 AC XY: 68595 AN XY: 74342

Gnomad4 AFR AF: 0.981

Gnomad4 AMR AF: 0.930

Gnomad4 ASJ AF: 0.822

Gnomad4 EAS AF: 0.930

Gnomad4 SAS AF: 0.890

Gnomad4 FIN AF: 0.920

Gnomad4 NFE AF: 0.894

Gnomad4 OTH AF: 0.904

Alfa AF: 0.910 Hom.: 7833

Bravo AF: 0.928

Asia WGS AF: 0.936 AC: 3258 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.5
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2906066; hg19: chr5-141580277;