rs9992272

Positions:

• chr4-176815982-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 0.707 in 152,036 control chromosomes in the GnomAD database, including 40,923 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 0.71 (40923 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.149

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.965 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: 0.707 AC: 107381 AN: 151918 Hom.: 40914 Cov.: 32

Gnomad AFR AF: 0.395

Gnomad AMI AF: 0.930

Gnomad AMR AF: 0.773

Gnomad ASJ AF: 0.860

Gnomad EAS AF: 0.987

Gnomad SAS AF: 0.811

Gnomad FIN AF: 0.815

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.824

Gnomad OTH AF: 0.749

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

GnomAD4 genome AF: 0.707 AC: 107417 AN: 152036 Hom.: 40923 Cov.: 32 AF XY: 0.711 AC XY: 52836 AN XY: 74294

Gnomad4 AFR AF: 0.395

Gnomad4 AMR AF: 0.773

Gnomad4 ASJ AF: 0.860

Gnomad4 EAS AF: 0.987

Gnomad4 SAS AF: 0.812

Gnomad4 FIN AF: 0.815

Gnomad4 NFE AF: 0.824

Gnomad4 OTH AF: 0.752

Alfa AF: 0.813 Hom.: 103179

Bravo AF: 0.690

Asia WGS AF: 0.868 AC: 3019 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.89
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9992272; hg19: chr4-177737136;