rs1867347

Variant names:

• chr9-104010478-A-G
• rs1867347

Your query was ambiguous. Multiple possible variants found:

• chr9-104010478-A-G
• chr9-104010478-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 0.516 in 151,962 control chromosomes in the GnomAD database, including 20,849 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 0.52 (20849 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.143

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 = 0.776 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: 0.516 AC: 78281 AN: 151844 Hom.: 20822 Cov.: 32

Gnomad AFR AF: 0.599

Gnomad AMI AF: 0.270

Gnomad AMR AF: 0.526

Gnomad ASJ AF: 0.418

Gnomad EAS AF: 0.796

Gnomad SAS AF: 0.541

Gnomad FIN AF: 0.463

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.456

Gnomad OTH AF: 0.514

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

GnomAD4 genome AF: 0.516 AC: 78366 AN: 151962 Hom.: 20849 Cov.: 32 AF XY: 0.518 AC XY: 38445 AN XY: 74268

Gnomad4 AFR AF: 0.600

Gnomad4 AMR AF: 0.526

Gnomad4 ASJ AF: 0.418

Gnomad4 EAS AF: 0.796

Gnomad4 SAS AF: 0.539

Gnomad4 FIN AF: 0.463

Gnomad4 NFE AF: 0.456

Gnomad4 OTH AF: 0.514

Alfa AF: 0.466 Hom.: 35206

Bravo AF: 0.525

Asia WGS AF: 0.644 AC: 2242 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	4.6
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1867347; hg19: chr9-106772759;