rs4978053

Variant names:

• chr9-26208859-G-C
• rs4978053

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 0.0691 in 151,720 control chromosomes in the GnomAD database, including 432 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 0.069 (432 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.374
• Publications: 4 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 (AMR) allele frequency at 95% confidence interval = 0.0928 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: 0.0690 AC: 10462 AN: 151606 Hom.: 429 Cov.: 32

Gnomad AFR AF: 0.0909

Gnomad AMI AF: 0.0648

Gnomad AMR AF: 0.0964

Gnomad ASJ AF: 0.0173

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.0108

Gnomad FIN AF: 0.0411

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0660

Gnomad OTH AF: 0.0629

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

GnomAD4 genome AF: 0.0691 AC: 10479 AN: 151720 Hom.: 432 Cov.: 32 AF XY: 0.0649 AC XY: 4810 AN XY: 74160

African (AFR) AF: 0.0908 AC: 3760 AN: 41422

American (AMR) AF: 0.0970 AC: 1475 AN: 15212

Ashkenazi Jewish (ASJ) AF: 0.0173 AC: 60 AN: 3468

East Asian (EAS) AF: 0.00155 AC: 8 AN: 5174

South Asian (SAS) AF: 0.0110 AC: 53 AN: 4820

European-Finnish (FIN) AF: 0.0411 AC: 428 AN: 10402

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0660 AC: 4482 AN: 67916

Other (OTH) AF: 0.0628 AC: 132 AN: 2102

Alfa AF: 0.0628 Hom.: 172

Bravo AF: 0.0759

Asia WGS AF: 0.0170 AC: 60 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.3
DANN	Benign	0.69
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs4978053; hg19: chr9-26208857;