rs9437689

Variant names:

• chr1-95083980-C-T
• rs9437689

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 0.342 in 152,060 control chromosomes in the GnomAD database, including 10,384 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 0.34 (10384 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0810

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.42 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: 0.343 AC: 52064 AN: 151942 Hom.: 10383 Cov.: 33

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.376

Gnomad AMR AF: 0.361

Gnomad ASJ AF: 0.424

Gnomad EAS AF: 0.185

Gnomad SAS AF: 0.369

Gnomad FIN AF: 0.582

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.424

Gnomad OTH AF: 0.312

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

GnomAD4 genome AF: 0.342 AC: 52073 AN: 152060 Hom.: 10384 Cov.: 33 AF XY: 0.350 AC XY: 25996 AN XY: 74302

Gnomad4 AFR AF: 0.151

Gnomad4 AMR AF: 0.362

Gnomad4 ASJ AF: 0.424

Gnomad4 EAS AF: 0.185

Gnomad4 SAS AF: 0.368

Gnomad4 FIN AF: 0.582

Gnomad4 NFE AF: 0.424

Gnomad4 OTH AF: 0.313

Alfa AF: 0.405 Hom.: 10802

Bravo AF: 0.319

Asia WGS AF: 0.258 AC: 900 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	5.9
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9437689; hg19: chr1-95549536;