rs4977886

Variant names:

• chr9-23689719-C-A
• rs4977886

Your query was ambiguous. Multiple possible variants found:

• chr9-23689719-C-A
• chr9-23689719-C-G
• chr9-23689719-C-T

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 0.224 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
• Publications: 3 publications found

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.106 AC: 4415 AN: 41510

American (AMR) AF: 0.262 AC: 4007 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.223 AC: 771 AN: 3464

East Asian (EAS) AF: 0.113 AC: 586 AN: 5182

South Asian (SAS) AF: 0.135 AC: 653 AN: 4826

European-Finnish (FIN) AF: 0.345 AC: 3632 AN: 10538

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.284 AC: 19265 AN: 67944

Other (OTH) AF: 0.192 AC: 406 AN: 2110

Alfa AF: 0.255 Hom.: 10077

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
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs4977886; hg19: chr9-23689717;