chr9-26524686-C-T

Variant names:

• chr9-26524686-C-T
• rs4978076

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.504 AC: 20929 AN: 41504

American (AMR) AF: 0.431 AC: 6590 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.464 AC: 1608 AN: 3466

East Asian (EAS) AF: 0.128 AC: 661 AN: 5160

South Asian (SAS) AF: 0.561 AC: 2699 AN: 4814

European-Finnish (FIN) AF: 0.482 AC: 5079 AN: 10536

Middle Eastern (MID) AF: 0.565 AC: 165 AN: 292

European-Non Finnish (NFE) AF: 0.506 AC: 34378 AN: 67956

Other (OTH) AF: 0.447 AC: 942 AN: 2106

Alfa AF: 0.504 Hom.: 11380

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
PhyloP100		1.1

Splicing

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

Other links and lift over

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