9-80205963-T-C

Variant names:

• chr9-80205963-T-C
• rs1329554

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 0.739 in 151,968 control chromosomes in the GnomAD database, including 42,478 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 0.74 (42478 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.37

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 (EAS) allele frequency at 95% confidence interval = 0.929 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: 0.739 AC: 112169 AN: 151848 Hom.: 42415 Cov.: 31

Gnomad AFR AF: 0.879

Gnomad AMI AF: 0.586

Gnomad AMR AF: 0.772

Gnomad ASJ AF: 0.607

Gnomad EAS AF: 0.951

Gnomad SAS AF: 0.666

Gnomad FIN AF: 0.697

Gnomad MID AF: 0.529

Gnomad NFE AF: 0.652

Gnomad OTH AF: 0.696

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

GnomAD4 genome AF: 0.739 AC: 112293 AN: 151968 Hom.: 42478 Cov.: 31 AF XY: 0.741 AC XY: 55083 AN XY: 74288

Gnomad4 AFR AF: 0.879

Gnomad4 AMR AF: 0.772

Gnomad4 ASJ AF: 0.607

Gnomad4 EAS AF: 0.951

Gnomad4 SAS AF: 0.666

Gnomad4 FIN AF: 0.697

Gnomad4 NFE AF: 0.652

Gnomad4 OTH AF: 0.700

Alfa AF: 0.663 Hom.: 44134

Bravo AF: 0.751

Asia WGS AF: 0.824 AC: 2864 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	0.81
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1329554; hg19: chr9-82820878; COSMIC: COSV60364654;