rs3758354

Variant names:

• chr9-73149649-A-C
• rs3758354

Your query was ambiguous. Multiple possible variants found:

• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;