rs4400445

Positions:

• chr9-7558261-C-T

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 0.164 in 152,116 control chromosomes in the GnomAD database, including 2,162 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 0.16 (2162 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0820

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.169 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.164 AC: 24922 AN: 151996 Hom.: 2162 Cov.: 32

Gnomad AFR AF: 0.168

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.141

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.103

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.203

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.158

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

GnomAD4 genome AF: 0.164 AC: 24932 AN: 152116 Hom.: 2162 Cov.: 32 AF XY: 0.164 AC XY: 12190 AN XY: 74362

Gnomad4 AFR AF: 0.168

Gnomad4 AMR AF: 0.141

Gnomad4 ASJ AF: 0.103

Gnomad4 EAS AF: 0.102

Gnomad4 SAS AF: 0.132

Gnomad4 FIN AF: 0.203

Gnomad4 NFE AF: 0.172

Gnomad4 OTH AF: 0.162

Alfa AF: 0.166 Hom.: 3175

Bravo AF: 0.159

Asia WGS AF: 0.129 AC: 453 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.8
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: rs4400445; hg19: chr9-7558261;