9-105664781-C-T

Variant names:

• chr9-105664781-C-T
• rs1463984

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 0.132 in 152,078 control chromosomes in the GnomAD database, including 1,870 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 0.13 (1870 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.248
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.472 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: 0.132 AC: 20134 AN: 151960 Hom.: 1868 Cov.: 32

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.0407

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.123

Gnomad EAS AF: 0.486

Gnomad SAS AF: 0.160

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0780

Gnomad OTH AF: 0.137

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

GnomAD4 genome AF: 0.132 AC: 20149 AN: 152078 Hom.: 1870 Cov.: 32 AF XY: 0.139 AC XY: 10315 AN XY: 74332

African (AFR) AF: 0.172 AC: 7120 AN: 41450

American (AMR) AF: 0.153 AC: 2343 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.123 AC: 427 AN: 3466

East Asian (EAS) AF: 0.487 AC: 2524 AN: 5178

South Asian (SAS) AF: 0.159 AC: 769 AN: 4830

European-Finnish (FIN) AF: 0.123 AC: 1302 AN: 10548

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.0780 AC: 5305 AN: 68002

Other (OTH) AF: 0.139 AC: 293 AN: 2112

Alfa AF: 0.104 Hom.: 5454

Bravo AF: 0.139

Asia WGS AF: 0.304 AC: 1054 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.3
DANN	Benign	0.60
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs1463984; hg19: chr9-108427062;