rs144649413

chr9-103607662-G-A

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 0.102 in 124,432 control chromosomes in the GnomAD database, including 737 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 0.10 (737 hom., cov: 15)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.122 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: 0.102 AC: 12740 AN: 124318 Hom.: 738 Cov.: 15

Gnomad AFR AF: 0.0609

Gnomad AMI AF: 0.0801

Gnomad AMR AF: 0.0944

Gnomad ASJ AF: 0.190

Gnomad EAS AF: 0.131

Gnomad SAS AF: 0.0568

Gnomad FIN AF: 0.0815

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.124

Gnomad OTH AF: 0.113

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

GnomAD4 genome AF: 0.102 AC: 12743 AN: 124432 Hom.: 737 Cov.: 15 AF XY: 0.100 AC XY: 5946 AN XY: 59272

Gnomad4 AFR AF: 0.0608

Gnomad4 AMR AF: 0.0942

Gnomad4 ASJ AF: 0.190

Gnomad4 EAS AF: 0.131

Gnomad4 SAS AF: 0.0573

Gnomad4 FIN AF: 0.0815

Gnomad4 NFE AF: 0.124

Gnomad4 OTH AF: 0.112

Alfa AF: 0.116 Hom.: 128

Bravo AF: 0.0998

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	3.0
Dann	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs144649413; hg19: chr9-106369944;