rs4978076

Variant names:

• chr9-26524686-C-T
• rs4978076

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.484 in 152,024 control chromosomes in the GnomAD database, including 18,122 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 0.48 (18122 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.10

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.32).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.543 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: 0.484 AC: 73450 AN: 151906 Hom.: 18092 Cov.: 33

Gnomad AFR AF: 0.503

Gnomad AMI AF: 0.532

Gnomad AMR AF: 0.431

Gnomad ASJ AF: 0.464

Gnomad EAS AF: 0.128

Gnomad SAS AF: 0.560

Gnomad FIN AF: 0.482

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.506

Gnomad OTH AF: 0.451

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

GnomAD4 genome AF: 0.484 AC: 73533 AN: 152024 Hom.: 18122 Cov.: 33 AF XY: 0.480 AC XY: 35664 AN XY: 74286

Gnomad4 AFR AF: 0.504

Gnomad4 AMR AF: 0.431

Gnomad4 ASJ AF: 0.464

Gnomad4 EAS AF: 0.128

Gnomad4 SAS AF: 0.561

Gnomad4 FIN AF: 0.482

Gnomad4 NFE AF: 0.506

Gnomad4 OTH AF: 0.447

Alfa AF: 0.504 Hom.: 10410

Bravo AF: 0.474

Asia WGS AF: 0.395 AC: 1376 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.32
CADD	Benign	18
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4978076; hg19: chr9-26524684; COSMIC: COSV69455215;