9-80205963-T-C

Variant names:

• chr9-80205963-T-C
• rs1329554

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.879 AC: 36467 AN: 41498

American (AMR) AF: 0.772 AC: 11787 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.607 AC: 2103 AN: 3466

East Asian (EAS) AF: 0.951 AC: 4928 AN: 5180

South Asian (SAS) AF: 0.666 AC: 3208 AN: 4820

European-Finnish (FIN) AF: 0.697 AC: 7358 AN: 10552

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.652 AC: 44281 AN: 67872

Other (OTH) AF: 0.700 AC: 1476 AN: 2108

Alfa AF: 0.672 Hom.: 56729

Bravo AF: 0.751

Asia WGS AF: 0.824 AC: 2864 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.81
DANN	Benign	0.51
PhyloP100		-1.4

Splicing

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

Other links and lift over

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