rs1377197

chr9-21683806-T-C

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 0.162 in 152,168 control chromosomes in the GnomAD database, including 2,480 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 0.16 (2480 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.211

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 (NFE) allele frequency at 95% confidence interval = 0.23 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.162 AC: 24616 AN: 152050 Hom.: 2481 Cov.: 32

Gnomad AFR AF: 0.0488

Gnomad AMI AF: 0.218

Gnomad AMR AF: 0.189

Gnomad ASJ AF: 0.194

Gnomad EAS AF: 0.0123

Gnomad SAS AF: 0.158

Gnomad FIN AF: 0.171

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.233

Gnomad OTH AF: 0.165

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

GnomAD4 genome AF: 0.162 AC: 24615 AN: 152168 Hom.: 2480 Cov.: 32 AF XY: 0.159 AC XY: 11829 AN XY: 74378

Gnomad4 AFR AF: 0.0486

Gnomad4 AMR AF: 0.189

Gnomad4 ASJ AF: 0.194

Gnomad4 EAS AF: 0.0124

Gnomad4 SAS AF: 0.157

Gnomad4 FIN AF: 0.171

Gnomad4 NFE AF: 0.233

Gnomad4 OTH AF: 0.163

Alfa AF: 0.214 Hom.: 2415

Bravo AF: 0.154

Asia WGS AF: 0.106 AC: 368 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	7.4
Dann	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1377197; hg19: chr9-21683805;