rs4978076

Positions:

• chr9-26524686-C-T

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;