9-80205963-T-C

Position:

• chr9-80205963-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 0.739 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;