rs9729377

Variant names:

• chr1-84810967-T-C
• rs9729377

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 0.368 in 152,060 control chromosomes in the GnomAD database, including 11,291 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 0.37 (11291 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.11

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.517 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: 0.368 AC: 55907 AN: 151942 Hom.: 11280 Cov.: 32

Gnomad AFR AF: 0.523

Gnomad AMI AF: 0.358

Gnomad AMR AF: 0.283

Gnomad ASJ AF: 0.385

Gnomad EAS AF: 0.00424

Gnomad SAS AF: 0.280

Gnomad FIN AF: 0.262

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.342

Gnomad OTH AF: 0.363

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

GnomAD4 genome AF: 0.368 AC: 55953 AN: 152060 Hom.: 11291 Cov.: 32 AF XY: 0.359 AC XY: 26683 AN XY: 74338

Gnomad4 AFR AF: 0.523

Gnomad4 AMR AF: 0.283

Gnomad4 ASJ AF: 0.385

Gnomad4 EAS AF: 0.00444

Gnomad4 SAS AF: 0.279

Gnomad4 FIN AF: 0.262

Gnomad4 NFE AF: 0.342

Gnomad4 OTH AF: 0.361

Alfa AF: 0.348 Hom.: 12644

Bravo AF: 0.376

Asia WGS AF: 0.178 AC: 624 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.11
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9729377; hg19: chr1-85276650;