rs9992272

Variant names:

• chr4-176815982-G-A
• rs9992272

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 0.707 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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.395 AC: 16343 AN: 41410

American (AMR) AF: 0.773 AC: 11805 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.860 AC: 2984 AN: 3470

East Asian (EAS) AF: 0.987 AC: 5100 AN: 5166

South Asian (SAS) AF: 0.812 AC: 3912 AN: 4820

European-Finnish (FIN) AF: 0.815 AC: 8608 AN: 10560

Middle Eastern (MID) AF: 0.721 AC: 212 AN: 294

European-Non Finnish (NFE) AF: 0.824 AC: 56016 AN: 68014

Other (OTH) AF: 0.752 AC: 1589 AN: 2112

Alfa AF: 0.794 Hom.: 210022

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
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs9992272; hg19: chr4-177737136;