9-104960454-A-T

Variant names:

• chr9-104960454-A-T
• rs1962882

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 0.641 in 128,060 control chromosomes in the GnomAD database, including 27,196 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 0.64 (27196 hom., cov: 27)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.41
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.79 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: 0.641 AC: 81993 AN: 127930 Hom.: 27145 Cov.: 27

Gnomad AFR AF: 0.798

Gnomad AMI AF: 0.657

Gnomad AMR AF: 0.664

Gnomad ASJ AF: 0.664

Gnomad EAS AF: 0.444

Gnomad SAS AF: 0.608

Gnomad FIN AF: 0.613

Gnomad MID AF: 0.650

Gnomad NFE AF: 0.565

Gnomad OTH AF: 0.639

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

GnomAD4 genome AF: 0.641 AC: 82102 AN: 128060 Hom.: 27196 Cov.: 27 AF XY: 0.641 AC XY: 40249 AN XY: 62768

African (AFR) AF: 0.798 AC: 26999 AN: 33832

American (AMR) AF: 0.665 AC: 8770 AN: 13196

Ashkenazi Jewish (ASJ) AF: 0.664 AC: 1891 AN: 2848

East Asian (EAS) AF: 0.444 AC: 1977 AN: 4450

South Asian (SAS) AF: 0.607 AC: 2573 AN: 4240

European-Finnish (FIN) AF: 0.613 AC: 5478 AN: 8940

Middle Eastern (MID) AF: 0.661 AC: 152 AN: 230

European-Non Finnish (NFE) AF: 0.565 AC: 32591 AN: 57706

Other (OTH) AF: 0.629 AC: 1119 AN: 1778

Alfa AF: 0.634 Hom.: 2773

Bravo AF: 0.677

Asia WGS AF: 0.491 AC: 1463 AN: 2990

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.21
DANN	Benign	0.44
PhyloP100		-3.4

Splicing

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

Other links and lift over

dbSNP: rs1962882; hg19: chr9-107722735; COSMIC: COSV60387179;