9-21771242-T-C

Variant names:

• chr9-21771242-T-C
• rs1341866

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 0.346 in 152,026 control chromosomes in the GnomAD database, including 10,006 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 0.35 (10006 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.31

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.419 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: 0.346 AC: 52569 AN: 151906 Hom.: 9999 Cov.: 32

Gnomad AFR AF: 0.184

Gnomad AMI AF: 0.203

Gnomad AMR AF: 0.392

Gnomad ASJ AF: 0.384

Gnomad EAS AF: 0.433

Gnomad SAS AF: 0.269

Gnomad FIN AF: 0.418

Gnomad MID AF: 0.287

Gnomad NFE AF: 0.422

Gnomad OTH AF: 0.340

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

GnomAD4 genome AF: 0.346 AC: 52609 AN: 152026 Hom.: 10006 Cov.: 32 AF XY: 0.346 AC XY: 25685 AN XY: 74298

Gnomad4 AFR AF: 0.184

Gnomad4 AMR AF: 0.393

Gnomad4 ASJ AF: 0.384

Gnomad4 EAS AF: 0.434

Gnomad4 SAS AF: 0.270

Gnomad4 FIN AF: 0.418

Gnomad4 NFE AF: 0.422

Gnomad4 OTH AF: 0.344

Alfa AF: 0.397 Hom.: 6536

Bravo AF: 0.340

Asia WGS AF: 0.323 AC: 1123 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.23
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1341866; hg19: chr9-21771241;