rs4977886

Positions:

• chr9-23689719-C-A
• chr9-23689719-C-G
• chr9-23689719-C-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 0.224 in 152,046 control chromosomes in the GnomAD database, including 4,401 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 0.22 (4401 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.298

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.28 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: 0.224 AC: 33989 AN: 151928 Hom.: 4403 Cov.: 33

Gnomad AFR AF: 0.107

Gnomad AMI AF: 0.214

Gnomad AMR AF: 0.263

Gnomad ASJ AF: 0.223

Gnomad EAS AF: 0.114

Gnomad SAS AF: 0.134

Gnomad FIN AF: 0.345

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.284

Gnomad OTH AF: 0.194

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

GnomAD4 genome AF: 0.224 AC: 33987 AN: 152046 Hom.: 4401 Cov.: 33 AF XY: 0.224 AC XY: 16672 AN XY: 74318

Gnomad4 AFR AF: 0.106

Gnomad4 AMR AF: 0.262

Gnomad4 ASJ AF: 0.223

Gnomad4 EAS AF: 0.113

Gnomad4 SAS AF: 0.135

Gnomad4 FIN AF: 0.345

Gnomad4 NFE AF: 0.284

Gnomad4 OTH AF: 0.192

Alfa AF: 0.261 Hom.: 7780

Bravo AF: 0.215

Asia WGS AF: 0.116 AC: 405 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.5
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4977886; hg19: chr9-23689717;