9-81000403-T-C

Variant names:

• chr9-81000403-T-C
• rs2378554

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.597 in 152,004 control chromosomes in the GnomAD database, including 28,341 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 0.60 (28341 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.776 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: 0.597 AC: 90640 AN: 151886 Hom.: 28314 Cov.: 33

Gnomad AFR AF: 0.783

Gnomad AMI AF: 0.359

Gnomad AMR AF: 0.603

Gnomad ASJ AF: 0.616

Gnomad EAS AF: 0.731

Gnomad SAS AF: 0.689

Gnomad FIN AF: 0.524

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.478

Gnomad OTH AF: 0.611

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

GnomAD4 genome AF: 0.597 AC: 90724 AN: 152004 Hom.: 28341 Cov.: 33 AF XY: 0.603 AC XY: 44791 AN XY: 74324

Gnomad4 AFR AF: 0.783

Gnomad4 AMR AF: 0.603

Gnomad4 ASJ AF: 0.616

Gnomad4 EAS AF: 0.730

Gnomad4 SAS AF: 0.687

Gnomad4 FIN AF: 0.524

Gnomad4 NFE AF: 0.478

Gnomad4 OTH AF: 0.610

Alfa AF: 0.508 Hom.: 42021

Bravo AF: 0.610

Asia WGS AF: 0.708 AC: 2462 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.3
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2378554; hg19: chr9-83615318;