9-73701425-A-G

Position:

• chr9-73701425-A-G

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 0.406 in 151,490 control chromosomes in the GnomAD database, including 14,813 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 0.41 (14813 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.293

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 = 0.518 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: 0.406 AC: 61441 AN: 151372 Hom.: 14821 Cov.: 31

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.467

Gnomad AMR AF: 0.404

Gnomad ASJ AF: 0.645

Gnomad EAS AF: 0.506

Gnomad SAS AF: 0.518

Gnomad FIN AF: 0.546

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.522

Gnomad OTH AF: 0.457

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

GnomAD4 genome AF: 0.406 AC: 61440 AN: 151490 Hom.: 14813 Cov.: 31 AF XY: 0.411 AC XY: 30389 AN XY: 74028

Gnomad4 AFR AF: 0.130

Gnomad4 AMR AF: 0.403

Gnomad4 ASJ AF: 0.645

Gnomad4 EAS AF: 0.506

Gnomad4 SAS AF: 0.519

Gnomad4 FIN AF: 0.546

Gnomad4 NFE AF: 0.522

Gnomad4 OTH AF: 0.460

Alfa AF: 0.473 Hom.: 4545

Bravo AF: 0.384

Asia WGS AF: 0.489 AC: 1693 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.3
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11143665; hg19: chr9-76316341;