rs3758354

Positions:

• chr9-73149649-A-C
• chr9-73149649-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 0.0736 in 152,140 control chromosomes in the GnomAD database, including 509 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 0.074 (509 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.42

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.154 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: 0.0737 AC: 11201 AN: 152022 Hom.: 509 Cov.: 32

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.0373

Gnomad AMR AF: 0.0548

Gnomad ASJ AF: 0.0786

Gnomad EAS AF: 0.163

Gnomad SAS AF: 0.0513

Gnomad FIN AF: 0.0322

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0413

Gnomad OTH AF: 0.0684

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

GnomAD4 genome AF: 0.0736 AC: 11204 AN: 152140 Hom.: 509 Cov.: 32 AF XY: 0.0727 AC XY: 5405 AN XY: 74360

Gnomad4 AFR AF: 0.137

Gnomad4 AMR AF: 0.0548

Gnomad4 ASJ AF: 0.0786

Gnomad4 EAS AF: 0.163

Gnomad4 SAS AF: 0.0509

Gnomad4 FIN AF: 0.0322

Gnomad4 NFE AF: 0.0413

Gnomad4 OTH AF: 0.0668

Alfa AF: 0.0528 Hom.: 473

Bravo AF: 0.0816

Asia WGS AF: 0.104 AC: 363 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	5.7
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: rs3758354; hg19: chr9-75764565;