rs1634352

Variant names:

• chr9-78698904-A-G
• rs1634352

Your query was ambiguous. Multiple possible variants found:

• chr9-78698904-A-G
• chr9-78698904-A-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 0.266 in 152,080 control chromosomes in the GnomAD database, including 6,528 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 0.27 (6528 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.96

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.4 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: 0.266 AC: 40364 AN: 151962 Hom.: 6520 Cov.: 31

Gnomad AFR AF: 0.0848

Gnomad AMI AF: 0.539

Gnomad AMR AF: 0.369

Gnomad ASJ AF: 0.256

Gnomad EAS AF: 0.413

Gnomad SAS AF: 0.195

Gnomad FIN AF: 0.394

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.323

Gnomad OTH AF: 0.287

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

GnomAD4 genome AF: 0.266 AC: 40386 AN: 152080 Hom.: 6528 Cov.: 31 AF XY: 0.272 AC XY: 20182 AN XY: 74322

Gnomad4 AFR AF: 0.0847

Gnomad4 AMR AF: 0.369

Gnomad4 ASJ AF: 0.256

Gnomad4 EAS AF: 0.415

Gnomad4 SAS AF: 0.194

Gnomad4 FIN AF: 0.394

Gnomad4 NFE AF: 0.323

Gnomad4 OTH AF: 0.291

Alfa AF: 0.300 Hom.: 3369

Bravo AF: 0.260

Asia WGS AF: 0.310 AC: 1076 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.033
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1634352; hg19: chr9-81313820;